Not really sure why Jules would even get pissed.
It may be a lie, but its not like its a deal breaker in a relationship.
You answered your first statement with your second. Of course she should be pissed...Shawn has kept this from here for YEARS now, and they're in a serious relationship. And nobody is saying it's a deal breaker and that their relationship will be over. I'd be surprised if that happened, and don't think it will at all. But she has every right to be pissed that he has been hiding the truth from her for so long.