Projectiles are good weapons in 4.87 and the devs are trying to figure out ways to balance their use. Seems to me, this is a good opportunity to add cargo usage to the ammunition, and let them be self-balancing that way.
CM, 0u (the only one that's zero)
Mine, 1u
Fighter missile, 1u
Fighter torpedo, 3u
Bomber missile, 1u
Bomber torpedo, 5u
Gunboat missile, 2u
Gunboat torpedo (Asco) 3u
Cruiser missile, 5u
Battleship missile, 10u
One thing about this, is that larger ships will be able to carry more ammo than smaller ships, which is "correct" from an RP POV.
Also, it will make it more difficult to have supply ships carrying ammo for the team.
Basically, if you want the payoff of a missile boat, then make room for the ammo. Otherwise use your energy weapons.