Would it be ok to wake up my previously cheating girlfriend in the middle of the night to ask her about emails from POF?
Why would you do that to your girlfriend?
Because she has been messaging guys on that dating website for a few months now
That was wrong of her to cheat. You should confront her and think about ending the relationship.
For her to know the pain of being betrayed. I told her to stop talking to people and look what happened.
I am sorry your girlfriend was cheating on you. You can only break it off and move on with your life. Ignore them and any remnants of them in the future, you deserve better.