Which mods effect VATs accuracy?

Any mod that increase the accuracy stat on the gun.

I saw early talks on the board that adding scopes seemed to decrease accuracy in VATS is this true or was it just wrong early guesswork?

I haven't noticed decreased VATS accuracy from adding scopes, but I have noticed increased AP usage in VATS from adding scopes that makes the added accuracy not terribly helpful (2 shots at 80% is better than 1 at 90%).

Personally I use reflex sights on anything I plan to use mainly in VATS (pistols and shotguns), and reserve scopes for sniping the old fashioned way only using VATS for a critical here and there.