Wily wouldn't nessesarily have to make clones of robots he created. He could just make more of them. After all, they're robots.
I'd say the Quint that died in W5 was the real Quint. Simply because I haven't heard anywhere they he was a clone and Quint hasn't been seen since. But even if he was the real Quint, that doesn't mean Wily couldn't just build him again if he wanted to. Shadowman, for instance, was made from an alien robot. You'd think something like that would be too unique to copy, but he reappears in the teleport stage, B&C, and PF. He also appeared in SAR, but RaMoon build him.
Maybe MM's weapon-hoding-thing was too full to allow him to steal the RM Killer's weapons on top of the Stardroids? The fact that there's legions of them inside of Wily's fortress is a look into World 5's story. I guess Wily finally smartened up and decided to make an army of his really good robots (Quint nonwithstanding, lol) in order to take over the world.