If I sign onto my daughters ipad iMessage, does an alert go somewhere, email or text message that her iPad Apple ID was logged onto from her iPad?
You could give "Restrictions" a shot. It's Apple's version of parental controls. Include Messages in the "Not Allowed" and set a pin. When your daughter tries to login to iMessage it'll clock failed pin tries and eventually lock her out of the restrictions area for a certain amount of time but not out of the actual iPad.
Edit: I just noticed FaceTime is on the preset list but iMessage is not.
So the answer to your question is to log her off iMessage and then go to restrictions and toggle Account Changes to "Don't Allow Changes"