Why do Super Mutants have weapon parts instead of guns when I kill them?

That’s because Super Mutants can only use guns that are rigged to one of maybe five vanilla animation sets, and we didn’t want to deal with vanilla-rigged receivers getting into players’ hands and generating largely bogus bug reports.

If it breaks your immersion, try thinking of it this way: When you kill the Super Mutant, they become so enraged that a “puny little human” beat them, so they clench their fists in anger, destroying the guns and leaving only parts of the weapon behind.