Because comics are nuts, I dunno if you mean literal clones or characters who fit the term in a general way. Hank Henshaw, Eradicator, and Kon-El are literal clones and that similarity was part of the point. Kon is obviously just about the opposite from Hank, and the similarities with Eradicator play into the bond between them. Bizarro's also another literal clone... but at the time of Reign, the only Bizarro to exist died years before, and the second was still over a year away.
Villain-wise, Zod and other Kryptonian characters weren't around at the same time. The Cyborg Superman being Hank seems like it would have been a cool surprise, because it was such a random (to me) revival, but I definitely wasn't reading back then. By the time other Kryptonians came about Hank basically abandoned his costume for that rust colored armor. Metallo had just returned in his Terminator mode, where he didn't use Kryptonite. He was basically just muscle so I wouldn't have called him "technological" until the electric years when Superman also had a funky way about technology. Brainiac just lost his (funny but) tragic angle and became a super tough space alien serial villain. All that just to say that redundancy would have to consider that he was really unique before the others. I always liked this part as a point of Superman's view concerning Hank and again, I think #999 was just full circle:
And then there was Zor-el. Now that Jor-el is back it seems less crazy but Cyborg Superman Zor was pretty bad. And I say that as someone who deeply liked that Supergirl era. I still very much support Silver Banshee as her frenemy, and I think Tyco and the Worldkillers deserved better. So did that space academy. Morrison had the coolest "new" villains, but maybe more than Hank you couldn't just give his characters to others and expect it to be as good. You'd probably have some bad dentist jokes with Xa-Du at least.