Maybe the missiles could be made into full subsystems/turrets so that they could be scripted (in the mission) to be "destroyed" when fired by the player and set back to 100% strength if a support ship docks with the player. If the weapon is big enough to be clearly visible, it would usually be a bomb anyway, so you could only carry a few of those at a time. However, all this would take a lot of effort and it would only work if you are using the appropriate ship and weapons.
Actually, this brings me to a sexp request that I have been thinking about for some time. I would basically like some event operators that determine whether or not a ship is of a given class and is carrying specified weaponry. Something like is-ship-class and is-ship-carrying-weapon. This would be useful for giving ship/loadout-specific orders to wingmen, whose ships and weapons can be changed around by the player and so are not known in advance by the mission designer. I have one or two places in PI where I could use the weapon one in particular.
The SCP releases now have pretty much all the major features I wanted in the original game and all I would really like to see are the the beam shield damage and event repeat bugs fixed and the memory issues dealt with. The only other addition I can think of is the ability to make missions without suns; currently, if no sun is specified in a mission, the game still puts one in somewhere.