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Now that we got Adeptus Custodes codex (which turned out not to be Talons of the Emperor book contrary to what I expected after recent black library titles provided very strong lore for Custodes and Sisters being meant for each other like bread and butter), we can dream about Plastic Sisters codex for SoS.

Both the tyranids' shadow and orks' waagh are warp-based.
Shall pariah units like silent sisterhood and culexus assassins affect these things in game?

How would it be possible to implement this?

I think the simpliest way is to just give SoS Ld-reducing aura like Night Lords CSM Legion has.
-1Ld to other units within 6" up to -3 total.

Massive waagh would not be affected, synapse is too strong to shatter, but it is still pretty.

The Tyranid Shadow is NOT warp based. At least not like your thinking.

The Tyranids Hive Mind connection through the synaptic web is not really warp based at all. And in previous editions Nids could not Perils with their Powers of the Hive Mind because of this. Further, the Shadow is not something that the Tyranids actively produce (though the hive mind has created creatures to boost it's effects as a weapon). It's a side effect of the synaptic web and an aura that blankets entire star systems since it covers a planet days to weeks before the tyranids actually arrive. No amount of sister of silence would have any impact on something like that. That would be like sisters of silence preventing warp storms.