That... is actually a really interesting question. Hm. It's a bit late for me to whip up a test game (at least with work tomorrow morning), so I'm tempted to say that you should just wing it. After all, nothing is more dull to read about in an AAR than a string of bland, by-the-book victories.
I tested it now (didn't occur to me before to just start a new game and spacemaster my stuff
). It works, at least when you shoot at a waypoint. The funniest thing: I didn't use boxlaunchers in my "just an engine, missiles, launcher, and a firecontrol" test FAC, and not only the missiles kept on going, but the FAC even kept on firing while in the mothership
The battle will be the finale battle (or rather, it will be the final war, as I have no idea where about 100 21kt ships and assorted smaller ones are), and the enemy fleet is way bigger than ours. Those FACs that are going to carry the size 20 launcher are made only to bring those missiles to the battlefield. I won't have many of these missiles anyway. So I am fine with shooting, returning to the hangar for the 2 1/2 hour reloading and then going out again instead of shooting, waiting 6h for the missiles to arrive and then reloading for 2 1/2 hours. I will have to see how many of the FACs I can crank out in 6 months, the shipyard only just finished, so it only has one slipway anyway.
The enemy fleet is way bigger than mine and I have never fought an NPR before.
Of course, I will not use the fact that they keep on shooting while in the carrier.