So is Clark hypnotized or not? I'm a little confused. But I guess all will be explained soon.

And about Superman being hypnotized in the original epi... Well, there was quite a bit in that episode that flew in the face of science. As far as I know, a person who has been hypnotized will not do anything that directly contradicts their ethics/personality/whatever. ie, you can't hypnotize Superman and get him to lock Lois in a water tank because his subconscious would not allow him to do that, regardless of who is controlling him.

But then again, this is LnC, so maybe that doesn't really matter