This is a question that dogs every incarnation of Superman, regardless of who it is. For instance, Clark has a close working relationship with Lois, Jimmy and Perry White, but they never recognize it's Superman.
If I wanted to answer the question, and resolve so many of the using superpower issues, I'd make it one of Clark's powers that he can cloud the mind, limitedly, when he's Superman.
Lex doesn't see Clark at all during the time Clark's at college and traveling the world, and has been so busy that he barely recognizes Clark Kent, reporter. Meanwhile, Clark's doing all the things he usually does in the comics - different posture, speaking in a lower register and with a slightly different accent - all that stuff.
In the books nad comics they claim that when Superman is Clark he has bad posture, walks funny, talks diffrent and all of these amazing subtle diffrences that throw everyone off track. Of course no one ever draws Clark like a scezzeball. You know if i was Superman I'd make Clark out to be a complete and total asshole or creep to really throw everyone off. Like spend time in porno shops during my lunch break, snezze on other people's food, giggle nervously. No one would suspect me then.
In the world of Smallville, with all the suspicions that Lex has about Clark, and all the incidents of supernatural happenings, there's no way that Lex wouldn't recognize Superman when he shows up. I doubt though that Smallville will carry the storyline that far.
Maybe Lex develops a stigmatism, and refuses to get it taken care of or get glasses? Hmmmmm?
This has always been a bone for people - Glasses are not a great disguise. Having said that, the movie handled it well! Chris Reeves played both characters with unique mannerisms, and the glasses really did make him look different! Can't say that for Tom Welling though...
Oh well, it's not just Lex that we need to consider, it's everyone else as well... Lana, Chloe, Lionel, and every other schmoe who has had any association with Clark.
(Assuming of course that they're still alive, and of sound mind. With the way that the characters seem to be taken out of commission, you can never tell...
When did the Joker ever know Bruce Wayne was Batman?
And Clark won't ever be friends with a killer like Lex becomes. Right now, Lex hasn't done anything terribly evil (that Clark knows about; whatever happened to Mrs. Luthor? If Clark knew Lex had sent her to her death, no way he'd let that stand), but he's destined to become Lex Luthor.
Superman and Clark Kent have different mannerisms, are different heights, have a different tone of voice, look like they have different builds, etc... When Clark is Clark he makes himself seem smaller and more frail and clumsy.
The movies even alluded to this once. They show Clark getting ready to reveal his secret to Lois, takes off his glasses and for lack of a better way to phrase it, he grows into Superman. They show him getting taller and his chest puffs out, etc. It's a really cool effect that went to show just how different the 2 really look.
Maybe the answer to this question is to just not overanalyze it and accept it for what it is -- a plot point that may not stand up to scrutiny in the real world but should be allowed in this fictional world.
Yes, in a Metropolis where Clark Kent was nothing but maybe a barely on the periphery reporter to Lex, its a lot easier to accept the fact that he would not make the connection.
But having been his best bud in Smallville and being very familiar with what Clark looks like without glasses... well willing suspension of disbelief and a spit curl only go so far.
As for Lana and the rest of the crowd it doesn't bother me as much... But Lex? Come on! It's one of those things that has bothered me ever since the show debuted. And I think the Super-Hypnotism went out in the comics about 20 years ago when they rebooted Supes.