I have seen AI fire missiles from the D6D and the MDC as well. The only noticable difference though is that they have fired usually from a range of 2 or less, and never from a distance. This has happened with ai vs ai and ai vs me in missions. If the ships do not go close range, they dont seem to fire their drones. Next time or 5 you see ai with drones vs you, try not firing and flying really close at slow speeds to see if they do.
Still haven't seen a single missile shot from my klingon enemies. the closest thing is the D7C (ai of course) dropping an SP on me.
even is I get upclose at slow speed I don't receive any missile shots. In fact the racks loading progress seems to be stuck at 50% and not moving. (I am close enough to see his phaser and disruptor reload progess moving, but not missiles)