So I had an idea. The main battle ships (destroyers, mainly) would be equipped with box launchers to add to their initial salvo, and then an array of conventional launchers for main combat. To accommodate this, the logistics vessel going along with them would have enough hangar space to fit one destroyer, and they would 'hot bunk' the hangar space, each taking turns to reload their boxes. It's a micromanagement nightmare, but something that could be thought about to make it less painful with some creative fleet designs, I'm sure.
Regardless, ammo becomes a concern. The logistics ships would be a large magazine carrier, so it would store ammo for the fleet. But I was also curious, if the logistics ship were stripped down, becoming just a flying hangar with no magazines, how would it handle reloads? If the docked ship has ammo in its stores, will the hangar ship draw from the docked ship to reload the box launchers? In other words, can a ship carry its own box launcher ammo, or does the ammo need to be on the loading platform?