I think that possibly the simplest way I can think of doing this is giving missiles launching weapons limited ammunition and a reload speed if they have ammo reserves. This allows players to dictate how they want to handle fire rate.
They can choose a slower but steady stream of fire, a large salvo with a long reload period, or a fast stream of fire with a short reload period before the stream starts up again.
Obviously, things like wing mounted missile pods or racks wouldn't have ammo reserves because duh, but this gives players flexibility in how they want to describe their missile use, as well as a way to limit the power of missiles to make sure that we don't end up with just missile spam everywhere.