Ok, forget what I said above. I played around a bit and MFs are still able to reload box-launchers.
Beware, however. When you order a ship with box-launchers to load ordnance from a planet (with maintenance facilities), you will get a "Orders Completed" message in the event log as soon as the ship reaches the planet. The fleet window will show 100% ammo and the individual ship screen will show the full ammo-loadout.
If you move the ship away from the planet before the TRUE reload time is over, the ship will be WITHOUT ammo. There also is no additional message, once the loading is realy finished.
So, take care.