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I can't believe she would fail to associate Clark's vulnerability to the Kryptonite that is all around.
If I remember correctly (and I skimmed through Weekend in Smallville, just to check) neither Lois nor Clark have encountered Kryptonite in this trilogy until now. So I find it perfectly plausible that Lois would not equate the green, glowing rocks on the warehouse floor with Clark's "inexplicable" vulnerability.

"You take turns, advise and protect one another, even heal or be healed when the going gets too tough. I know! That's not a game--that's friendship!" ~Shelly Mezzanoble, Confessions of a Part-Time Sorceress: A Girl's Guide to the Dungeons & Dragons Game

Darcy\'s Place