If we're going for missile realism a ship should be able to carry ammo that takes up cargo space (10 space apiece?) - on the flip side, missiles ought to track a lot better and move faster. Maybe I'm completely wrong, but in a traditional, RL sense missiles resond like CF mosquitoes, hit as hard as sunslayers, and take up a lot of room of a fighter's racks. If such a thing were done though, mines, torpedoes, and CDs would have to be seriously screwed around with too.
Alternatively, there's also the option of homing, energy weapons... but maybe I shouldn't go there. xD
Edit: this is bogus though btw m8s... why are we trying to change all these things when only a couple people think they aren't working?