As I said, I really do want to seal them away, but from a gameplay (not RP) perspective, I find that unwise. You're right, though, as I'm certainly powerful enough without the masks...but I don't know what perils the future has in store. Maybe the masks will be needed to fight an even greater evil, one so powerful that it can best Amadeus sans masks even on Adept difficulty! I'm certainly hoping for such an opportunity, so I think it best to keep the masks.
I don't think you can seal them away, even if you wanted to. Try dropping the mask on the floor and saving. You will find the mask in your inventory, or back on the floor of the ruin.