I notice the plasma torps the Romulans fire will take down my shields considerably.... then again almost any torpedo hit by any enemy takes my shields down WAY more than my own torpedos will do to theirs. I think there is something wrong with the way torpedos of any type work vs player shields.
The computer plays by a slightly different set of rules than the average human player, I've seen a single AI-Miranda disable two of my systems in the same engagement, what are the chances for that to happen?
So the reason consists of two words: "just because".
The "trick" for NPCs seem to be that they do full damage against shields with kinetic weapons. That makes Plasma Torps pretty devestating - even if you bring up a sliver of shields, it might not be enough.
I think that's pretty lame and deprives the game of an interesting gameplay aspect- trying to restore your shields just in time to defend against a torpedo hit.