Well, I agree that even though she's kissed Clark before doesn't mean that she's going to figure it out, since those kisses were under quite different circumstances and Lois wasn't "swept away by passion" quite like this.
But there were 3 kisses, don't forget - the first one was on the plane in SVFAP just before Trask threw her out.
And now that Lois has realized that she loved Clark too, subconsciously she may realize the connection...there are certainly any number of ways that the truth is going to come out, I imagine that Clark will probably get himself in a lot of trouble before the end of this story, and I'm looking forward to it immensely. (But, unlike Tank, I'm expecting a happy ending...)
Kathy