there are references to missiles being used on ships. it owould be interesting to see them incorporated into the game. the original starfleet battles had them (drones). it would not be the uberweapon one would think essentially it would be a Mirv heavy plasma or tricobalt. (take a tricobalt blast, divide by 6 and there you go. you can shoot it down or if you have the CIWS turret from thunderchild... it would but a whole new dynamic to PVP. a ship with a missle rack could target fighters or target carriers. carriers would ahve to choose between a hangar's fighters being attack craft or CAP.
The Borg and Ferengi used missiles, however the distinction between them and torpedoes doesn't really seem to be that great other than the visual effect used. Starfleet photon torpedoes eventually began to look like missiles but were still referred to as torpedoes.