He knew the option in the ship menu, and I have to agree it would be a bit too much if you happen to have a whole lane of missile based PDC.
Technically you could use a collier and use a command to supply to all PDCs from outside, but of course that would require you to build one if you don't happen to sport such design in your fleet plan.
Potential alternative: I once built a PDC with only box launching torpedoes, betting on the fact that the PDC would then reload automatically from planet supplies, just like ships with box launchers do. I had no enemy to verify that this worked though, but I guess it should. ...And if that works, then I guess the planet is somehow flagged as collier to begin with perhaps, meaning your PDCs might draw from them even with regular launchers (basically meaning that magazines on them are a waste of space and resource).
Again, PDCs see use so rarely, that I have never been able to test this out, but maybe someone has specialized experience in this here? A longstanding question of mine too.