I am so sorry that both of you are in this situation... That is truly awful...
I completely understand why you feel hurt by her not telling the truth about what happened. You *want* to be there for her- you obviously love her very much.
I have been sexually assaulted twice in my life, and stalked by the perpetrator the second time. It is terrifying, and what I experienced obviously doesn't hold a candle to what your wife went through with that ex.
I know it might not make sense, but she might feel ashamed of being raped. Like there was something she could/should have done to avoid it, or if she was a better person it wouldn't have happened, etc. She might be thinking that it was her fault she got raped and therefore she should deal with it on her own instead of burdening you. She might feel "dirty" and undeserving of support. She is probably experiencing PTSD and is probably not thinking as rationally as she normally would.
It sounds like she is going to need counseling, probably STD tests (and it sounds like pregnancy test as well), and God knows what else. If the test kit can give a positive ID on the rapist (sounds like the ex?) she may have to go through court to have him put away.
It is ok that you feel hurt. You are allowed to feel hurt that she didn't come to you with this, you really are.
I personally would suggest a gentle confrontation, saying that you know something happened and you just want to be there for her and that you love her no matter what it was. Unfortunately, saying that you feel hurt right now might not be very productive and might make her feel more distressed about her current situation.
I could not say whether you should express that feeling right away (and again, it is perfectly valid and understandable to feel that way- I'm not trying to say it is wrong or bad of you) but another poster might have better insight on that than me.
Ultimately though, it sounds like she is going to need a lot of love and help getting past this latest experience. Again, I am so sorry.