So, apparently, clicking the "update" button in the mod menu fixed the issue with the research costs...
At least most of it, just couple techs have increased research costs but not drastically, like thruster fuel tech taking agriculture packs now
It was on the MIR side probably, since I saw it being updated
I feel kinda dumb now
Though, error pop out with the removed tech persists:
https://imgur.com/a/NKRdFjk
Which weirds me out, since inserter capacity 8 doesn't exists in both with or without Simulacrius mod, as well as cannon and electric shooting speed tech
Laser shooting speed, research speed, weapon shooting speed, and worker robots storage still exists in the same level and research cost in both as well, perhaps research IDs got changed
Anyway, I'd consider the issue... solved. Thank you for your attention.