One of the reasons is that apparently, the "majority" of the Legio Cybernetica turned traitor, and now the modern Adeptus Mechanicus banned the old automata for fear of corruption. In fact, you can find this line in the 7th edition Adeptus Mechanicus codex, which explains why only Kastelan robots are used, and not the Heresy era (or Great Crusade era) automata.
Basically, they are tainted by association with the Dark Mechanicum, and by renegade Tech-priests who attempted to imbue their automata with Silica Animus or artificial intelligence, or daemons.
Way back in 1988, in both the White Dwarf issue 104, and Realms of Chaos: Slaves to Darkness, "many" Legio Cybernetica cohorts rebelled under the leadership of Warmaster Horus, and that parts of the Legio Cybernetica had been the first to declare for the Warmaster. The dishonored Legio Cybernetica Cohorts also fled to the Eye of Terror along with the Traitor Legions, and...as you remember, the whole "Legio Cybernetica has pledged itself anew to the Imperium and take binding oaths of loyalty more terrible than any Marine Chapter oaths." Funnily enough, in contrast to 7th edition, they have apparently regained the respect and admiration of everyone.
That's kind of hilarious, when you think about it. The lore keeps on changing. Anyway, why do fans think that the majority of the Legio Cybernetica turned? Back in the 1988 Realms of Chaos: Slaves to Darkness, there's a little tidbit of information that says this:
So more than half of the Adeptus Mechanicus, including many units of Legio Cybernetica, turned traitor. Hence, it is assumed that the majority of Legio Cybernetica cohorts turned traitor, and thus we have less 30K automata today. But take note that this nascent background lore has been changed and retconned over the years. In the past, "only those on Terra" remained loyal for the Collegia Titanica. That is no longer true, obviously, if you've been keeping up on Heresy lore and the Adeptus Titanicus or Legions Imperialis game. Roughly half of the Imperium's Titan Legions remained loyal, so that we can have more even games. Legio Atarus, for example, or Legio Astraman, Legio Crucius and Legio Fortis, do not originate from Terra. So yeah. The game lore has developed greatly since.
However, this was changed a little as the lore on robots developed. In 2012, when Horus Heresy was developed as a game by Forge World and the mythology was expanded upon, they no longer had "more than half" or the majority. Hell, the Adeptus Mechanicus was changed to the "Mechanicum" during the Heresy, and only became the Adeptus Mechanicus after the Binary Succession.
Again, this was to explain that the Loyalists are not necessarily outnumbered, and anyone can be a Loyalist, including Legio Cybernetica. Of course, it is undeniable that many cohorts turned Traitor and declared for the Warmaster, but there were at least equally many that did not.
However, it has always been assumed that those who turned Traitor outnumbered the Loyalists, despite the changes in lore. I mean, that's not a wrong assumption, and judging from how it has developed from the 1980s, I think originally, that was intended to be the case.
Then The Rise of the Dark Mechanicum came.
What is interesting, in terms of rules, is that you cannot take any automata units in a Dark Mechanicum army. This is deliberately intended. I believe this is made to help differentiate Loyalists and Traitors further. This is not to say that if you're of Traitor allegiance, you're completely barred from using automata - far from it - but you're discouraged from using them and relying more on Stalkers to have that visual distinction between Loyalist and Traitor.
Right from the outset, we have this clash between Stalker Constructus and Loyalist Cybernetica automata.
If you remember, the Silica Animus was banned because AI and the Men of Iron and the Crimson Accords of Mars. The Emperor forbade research and construction of artificial intelligence. This was the reason why so many Cybernetica Tech-priests turned to the Warmaster - they wanted to see these restrictions lifted.
At the same time, Animus Inimica is a very telling name - Inimica, as in inimical. Something that is utterly hostile and dangerous toward Animus, which means mind or spirit. Don't ask me why they use silica (which means hard stone or flint) for artificial because Silica Animus is supposed to mean artificial mind/spirit (but it roughly translates to hard stone spirit/mind in Latin). Maybe it's short form for Simulacra? Would make more sense, really. Anyway, I believe the word Inimica is used intentionally, to serve as a contrast against the automata. Of course, this isn't the official name of the Stalker constructs. They are known as Silica Mutus, which I'll get into later. Mutus, by the way, relating to "mutate" or "mutatis mutandis," which is a reference to mutation or change - hence hard stone mutant in Latin. Roughly. Don't ask me who came up with these pseudo-Latin names. Anyway, Anima Inimica is used to describe the passage or scene where the Stalker constructs confront the Cybernetica automata for the first time.
Basically, Dark Mechanicum Stalker constructs are inimical toward Mechanicum automata. And this, I believe, is Games Workshop's attempt to distinguish between Loyalist Mechanicum and Dark Mechanicum, but at the same time not invalidating the already existing Traitor Cybernetica cohorts that fans own or in the lore. So yes, you can still run automata if you're Traitor, but you're given more incentives to run a Dark Mechanicum force of Stalkers without automata, and you're encouraged to have automata as Loyalist - thematically speaking. This has nothing to do with balance or gameplay, so you don't get bonuses for running automata as Loyalists. Instead, you're less restricted, whereas if you play Dark Mechanicum, you are restricted to taking automata as part of your 30% limit of allies. Basically, you've to take an allied Mechanicum detachment, so you're discouraged but not banned from taking automata.
Lorewise, it's also worth noting that the Stalker constructs are so hostile toward automata that they actively seek them out to eliminate them, breaking off from Legio Mortis's main advance toward Magma City, just so they can engage and exterminate Macro-cohort Exsomnis, a war host of Legio Cybernetica.
The Stalker constructs, rather than being known as Silica Animus, is officially categorized as Silica Mutus.
Long story short, they are utilized by those Forge Worlds who lack ties to the Legio Cybernetica, to shore up their weaknesses and lack of heavy war engines. There is a major shift in the militant base of the Traitor Mechanicum, as they manufactured Stalker constructs in favor of the more ancient and closely guarded automata of the Legio Cybernetica, which remains under the close purview of that militant arm, with their own loyalties and agendas, and requiring political favors and other oaths or bonds from those requesting for Cybernetica assistance. In contrast, the blueprints for the Stalker constructs were disseminated freely, allowing these Forge Worlds without ties to the Legio Cybernetica, to construct their own war engines without relying on political favors and goodwill.
These are different from daemon engines. Rather, Stalker constructs appear to be produced by combining the techniques of Legio Cybernetica with aurum nerve bundles that mimicked synapse clusters found within higher mammals, creating a lesser synthetic life that is more advanced and less restrained than traditional battle-automata.
So Stalkers are effectively meant to replace Cybernetica automata in Dark Mechanicum lists. Again, that doesn't mean you can't field Cybernetica automata if you're Traitor, it just means you're more restricted in doing so, as they're meant to contrast each other and visually distinguish the Loyalist from the Traitor. Sort of like Thousand Sons versus Space Wolves, where you can play either faction as Loyalist or Traitor, but from a glance, a third party can tell apart the two armies (even though they're both Legiones Astartes). Also, they're meant to hate each other with a burning passion (you'll never see them allied thematically, unless there's a Barabas Dantioch and Alexis Pollux moment), so again, you'd hardly see them in the same army unless allied Magi bring their two separate detachments together. But I imagine they would have to rein in their automata from attacking each other outright. This is probably speculation for now, but I believe the machine-spirits of the Cybernetica automata are hostile toward the ravenous Stalker constructs, and would seek to destroy them if it were not for their Magi holding them back.
I'm not sure if what I'm saying makes sense?
Anyway, I'm not sure if this counts as a soft "retcon" of existing Cybernetica lore, but evidently, the Cybernetica automata is gradually being marked as a symbol or representation for Loyalists in the face of Stalker constructs for the Traitor Dark Mechanicum. This, obviously, only applies to Legions Imperialis at the moment because we don't have any plastic Stalker construct models for 28mm scale Horus Heresy. We'll be getting them eventually, far down the future, as plastic production techniques, CAD and manufacturing technology improve, but for now, aside from Legions Imperialis, automata remain firmly in the province of both camps.
That said, I'm detecting a gradual shift - a soft "recton," as I put it - toward distinguishing Cybernetica automata for Loyalists as a foil against the Dark Mechanicum Stalker constructs. Of course, you can still play Traitor Mechanicum with lots of automata, perhaps as Legiones Auxiliary Cybernetica or alongside Traitor Knight Houses and Titan Legions, but they would be Traitor Mechanicum as opposed to being Traitor Dark Mechanicum. This is to represent those Magi who have sworn to Horus's banner, but haven't gone down the road of constructing Stalkers - not that they need to because they already have Cybernetica automata for that role.
