Update. She still denies an EA. But the signs are all there. She would call him whenever I was out of town, then of course the nude pics. When I originally confronted her she was angry that I spied on her. Then said things to me like "I need space", "You're smothering me", "We have nothing in common".
She continues to tell me she loves me and there was nothing going on and I have nothing to worry about. I confronted her about the fact that he was still her Facebook "friend". She got angry again, and said she forgot (his name and icon appear on the side of her Facebook page. Every time she would show me something on Facebook I would see it). I told her I would not tolerate it and she has now "unfriended" him.
She may just be hiding it better. I don't know. She seems more distant. She hugs me but nothing more intimate than that and a kiss. She used to talk about wanting us to get away together (no kids), now when I bring it up all she talks about is bringing our son (13yrs).
I am trying to remain cool but it's hard. I have to go on a trip the end of the month and I fear she will be in contact with him.