They also sometimes arm them. I saw the Drengin AI making transports with attacks of over 100 in one game. Offhand, I can't think of a bigger waste of resources.
Dear Citizen Purge, I have to question the 'waste' portion of this. I have tried the tactic successfully in some of my games, where I didn't want to be bothered with a minor race getting uppity - a blackhole missle gun on a huge hull with sufficient protection and speed to wipe the offender out works well on auto-attack (if he's the only one at war with you. It goes immediately to the pikes home planet kills all his ships and invades. Saves me having to do it manually for a minor irritant. But generally I think your right.