This reminds me of Descent 2, where the cutscenes always show four Concussion Missiles strapped to your ship, even though your ship can carry way, way more armament than that -- and the ingame model always shows two giant mystery missiles regardless of how many secondaries you are actually carrying.
If we're going to pull the realism card, have we tried visualizing where the hundreds of missiles in any given FreeSpace fighter are crammed?
Ace Combat solves the "more missiles than visually reasonable" problem by simply having more missiles magically appear on their pylons after they are fired. Maybe by using animation code and having correct missile models sticking out of ships, firing missiles could have new missiles "push out" and load into position. *puts a nuclear symbol on a searchlight and beams it at the sky*