Lana putting all the pieces of the puzzle together, except the first one she got.

[elway]

She was told by Lionel that "they" have a weakness (kryptonite). In regards to the 2 from the black ship. Now if she can put 2 and 2 together she have the truth to the weakness. Atleast you'd think she'd remember a little of that. And not be absolutley clueless to it. Especially after Chloe said he dose "have 1 weakness"
I beleive Lionel said the same about Nam ek and Atherny(sp).

And she should start to be putting the pieces together about CK's real name (Kal-El). She heard the bar tender call him Kal in S3 and the 2 from the ship were looking for Kal-El when they got to earth.

I guess she thinks he's just one big dumb adopted krypto freak huh?

[Kal-alien]

I think she'll put it together soon. And as soon as she gets the name she'll figure out the rest of his secret (The Alien Part) and his therefore his weakness. or maybe it'll happen in the reverse order. I don't know I'm not Miss Cleo.

[Ultron]

Lana probably believes Clark is a meteor freak, not an alien. Seeing as meteor freaks are a dime a dozen on Smallville.