I had a running entry in the earlier requests threads about any interaction between Lex and Clark himself just because I couldn't imagine Lex not figuring it out (if he actually paid a simpering sod like Kent any mind, a point A-SS #5 illustrated). I'd never imagine he'd actually do anything about it, Luthor's a sonnuva bitch, but I've always figured him to have some level of class.
So to have him know is an interesting point, but to have it dropped in his lap like this isn't something I really dig (though yeah, like a poster above said, his pride would totally keep him from acting on the knowledge because of that fact).