If people really want to start spicing up munitions (missiles and such) - then maybe consider giving munitions a cargo value?
This way - smaller ships could carry the same size torps as a bomber (or even a capital ship) - but less of them, as they would be balanced by their cargo holds.
Look at a Tomahawk Cruise Missile - what is the difference between one that is carried by a fighter jet, a strategic bomber and a naval frigate?
The answer is of course NONE, just that the different vessels carry different numbers of them. Cargo stats could be adjusted slightly, so that two bombers or SHFs might carry as much as 4 VHFs, or 6 HFs. It means that Freighters could be made into missile boats simply by assigning the correct guns and ammo.
It also means that munitions could be made into tradeable commodities in their own right!