It's not hair on the mako rejects, it's spikes. If you play Crisis Core this becomes extra obvious as you fight like 5 of them.

I don't think there's any real reason to doubt cloud is cloud, especially since that would negate his whole revelation in FF7.
And if he was replaced with one, why wasn't Zack? And why would they even want cloud if they could duplicate a person with one of the abominations, after all, Zack is the most powerful thing Hojo has ever created, it wouldn't make sense to not duplicate him over and over if they could.