oh man.. it seems that if you use the 'clear all' button in the ord management, it doesn't refresh, but if you close individual unit window and go back in, the tubes are all empty.... but the missiles have completely disappeared as well. they've not gone back into stock. this is with a box launcher. while docked. the stock of missiles on the mothership has not increased either.
Edit:
Ah I see, these were actually empty since they'd fired before.
Magazine contents includes those assigned to launchers.