The short answer is that it's one of those lines in which FFC and Puzo took some dramatic liberty with the script. They want us to believe that the Mafia is omnipotent--so Clemenza can, on demand, provide a gun that is untraceable, and he has some kind of magic tape that doesn't attract fingerprints. But the real point is to reinforce that, in order for Michael to literally get away with murder, he can't be connected with the gun in any way. That's why Clemenza (and later, Sonny) kept emphasizing that Michael had to drop the gun after using it. And, of course, his prints can't be left on the gun.

"Magic tape" or no, in reality, the gun could have been wiped down with alcohol or oil to erase existing prints. Michael could have grasped the gun with a handkerchief when removing it, then wrapped the handkerchief around the gun butt before leaving the john. "Untraceable" isn't as difficult as you might imagine. If the gun had been stolen from a big shipment from the factory years earlier, and never registered with any individual, it wouldn't be traceable to anyone.