It was shown in SUPERMAN #4 that Lois knows that Clark is in Smallville visiting his parents' grave. Also there was a panel in the same issue that shows that Lois is like monitoring the cemetery where Superman just been at.
In Superman #5, When Superman dropped McCoy from the top of Daily Planet, Lois shouted Clark.
Is she having thoughts that Clark might be Superman? If so, what do you think will happen to Lois if Geoff John is really planning to pair WW and Supes?