Noone ever said stock was set up reasonably.
I think it is extremely unreasonable to think that you can just power a gigantic wave motion gun from excess engine energy. It has to pull a lot more energy than that, thus increasing fuel/supply consumption when used. You could assume it does draw energy from the main reactor powering the engines, but it still is going to draw relatively more than anything like a dvd player in a modern car does.
How would bullets and missiles be useful to stock a wave motion gun?
If you look at a DUC, it uses both. The ordnance is the actual physical bullets, and the supply usage is the energy it takes to accelerate those bullets to near-light speeds. If you normalize its supply usage to that of the WMG, it uses about 18 supplies compared to 30 for the WMG. Maybe it shouldn't use quite so many supplies since all it is likely doing is powering up some electromagnets, but I can still see it taking some non-zero amount of supplies to fire.
Then look at missiles. They should probably only require ordnance, or at least very low supplies, because it doesn't take much energy to launch them compared to what you would need to generate a "high intensity fusion beam." Presumably, they should be able to use their own fuel to accelerate.