The wards were to stop someone going through the door. Noone knows yet how to ward against traveling especially in the White Tower where no one knew how to travel.
As for why it was still sitting on a shelf waiting for Egwene, Before Mesanna could take the rod she would have to know it is there, and exactly what room it is in. The WT has been collecting objects of power for a few thousand years; it is probably safe to assume that they fill more than just a single room. Just knowing what room it is in would be a hurdle, if she knew of the rod's existence.
Mesanna is arrogant. She didn't choose the tower as a base of operations so that she could learn all the tower's secrets, but to prove how inferior to her they are. Why would she waste her time learning the tales of glorious actions of the past Amerlyns. She didn't take it because she was too arrogant to find out it was there.