I'm sorry you found what you did, that would eat me up inside.
Her past aside, if you guys have been together 6 months, maybe it's time to talk about your sexual past, at least for your own safety. With the two of them sleeping together in between relationships, that could potentially be a lot of stds and such floating around between all of you. Ick. And maybe there isn't, but you NEVER know, especially when this has been going on a few years.
I also agree that i don't think he took advantage of her or treated her like a prostitute. She made a conscious choice to continue having this thing with him over time. She made a choice to travel to see him, and no one forced her to have cyber sex with him. In my opinion, the chances that she doesn't have feelings for him are pretty slim— like someone else mentioned, many women who think they can handle f-buddies in reality can't, and I've never known a woman to travel to another state JUST for sex. I think that's crap. I have a hard time believing she doesn't harbor any feeling for him at all. The reason i would be cautious of that is because if there is something, on her end for the f-buddy, 6 months ago isn't all that long ago and things are still very fresh.
If you have a conversation about your sexual past, and she fails to mention this guy, I would be very concerned, because then she's legitimately hiding something, for some reason unknown to us. And if she's not ashamed about it for any reason and there's nothing to hide, I see no reason why she wouldn't tell you. If she doesn't mention it, you may shoot yourself in the foot in doing it, but maybe then is the time to tell her the truth, that you know about her f-buddy and (calmly) ask her why she didn't tell you about it... Maybe two wrongs will cancel each other out and make a right, and you'll both feel stupid for lying and snooping, and it will put you both in a new place to be honest with each other to start fresh. Or maybe she'll be pissed and you will break up :\
I'm not sure what other way you can extract the truth out of her without continuing to snoop, other than this. It is a bit of game playing, but on the other hand, I would feel really grossed out knowing the person I'm with could possibly be passing something around to me and didn't care to tell me there was a potential risk to me. As my friend Dr. Phil says, people with nothing to hide- hide nothing. But this shouldn't be tit-for-tat. Just because you found out about this, doesn't give you the right to snoop. But I still think you deserve to have some answers because of the sexually-related risks.
Maybe you can sit down and say that you did something you shouldn't have, and you feel guilty about it, and ask her if there's anything she'd like to tell you about ________ (enter f-buddy chat name here). Maybe she'll just come forward about it all and will tell you the truth, and not even flinch and just say it never came up in convo. Maybe she'll say she has feelings for him. We can't predict anything, but you have to take that risk now that YOU have done something wrong,
Regardless, I think you need to come up with a plan of some sort. You can have all of this jumbling around in your head — it'll make you crazy!
Good luck!