It would be really nice to allow the capship to start building them as soon as there is an open spot in the missile bay.
Say your capship can stock 100 missiles in it's missile bay.
Then when you fire one, production is started to replace the fired missile.
Eventually all 100 will have been fired but are already replaced by 50 or so, as production doesn't go as fast as firing them.
In the end, you might end up out of missiles. This makes the capship a bit vulnerable and adds a strategy element: time to withdraw from battle, at least until enough missiles have been replaced.
Or you might end up without the required resources, which also makes you run out of missiles because you can't produce any more.