Actually, I believe many have pointed out that the original schematics for the Klingon battle cruiser from TOS had missiles on it, that is where ADB got the missiles thing from they didn't just pull it out of thin air. I also believe that the Feringi have fired missiles/drones off on screen, haven't they? Plus there was mention of a very large missile thing that the Cardassians used, I believe.
I agree about the sound effects and visuals of the weapons. That was one of my bigger beefs, you just don't feel like you are doing much when you fire in SFC3. In the previous installments, you would let off a load and it sounded like you were unleashing a load on the guy, and his ship would light up, icons flashing and stuff. Much more satisfying for a gamer, imo.