The engine is what limits the ammo capacity if I'm not mistaken. As such, it cannot be altered between ships.
Furthermore, the extra ammo could be just controlled by cargo space, most would say. Problem there is most fighters then mounting CDs would have a very hard time carrying anything BUT CDs. As such, its not the best idea.
I believe torpedos already take cargo, which helps to limit their effectiveness.
Also, last time I checked, most pilots rarely use up 70 missiles in an engagement, if I'm not mistaken. Even so, a restock of even 20 more missiles would be sufficient unless it happened to be one fighter and captial vs a ton of fighters. In which case, how would it help any more?
The idea is nice, but again, limited due to the engine. Unless, I am wrong (wont be the first time) and somoene can point out in the ini.s where a ship's ammo capacity can be modded.
EDIT: What it can, however, be useful is more than 70 CMs, in which case thats understandable. But in 9/10 encounters, I use CMs about 3x faster than missiles, and I still dont run out of CM unless its extremely hairy. I'd say for every one missile I shoot, I drop about 5 cm on average.