Also, since your Capital Ship Missle component is larger than your other low-tech weapons, it could be assumed that some of this extra space is missle storage.
As far as the fact that you can fire missles indefinetly combat round ofter combat round, the next patch will deal with this somewhat as wepons will no longer fire once a ship has depleted all it's supply.
You could also take a Trek perspective on this and assume some sort of replicator technology that produces missles, or any other ammo for that matter. This actually makes some amount of sense considering all weapons, engines, and other devices in SE4 use the same mysterious "supply" substance. Call it liquid hydrogen, or anti matter, or whatever you want. It gets converted into energy for the engines, or molecularly combined into ammo for the weapons, or changed into food for the crew.
Geoschmo