First step: Make sure the F5 Ordinance tab is showing what missile loadout is supposed to be on the ship (each class, the FAC, the carrier, etc). If its showing no missiles, then 0% is exactly what is supposed to happen.
Set the loadout for the class (do this when designing the ship, and after updating your missiles to new designs). Then when you click the population/mothership/collier buttons, the system will look at the assigned loadout, and select those missiles (if in stock).