The secrets she keeps from the kid have little to do with you. Some people keep this sort of thing from kids. Perhaps they never think they are old enough to understand. Still, if you have doubts about her, why bother. It's no fun being in relationships with people you don't trust.
Bad! Kids are smart and they figure things out sooner or later. They will have far more respect for her and you if she is honest and up front about it.
As long as she assures him that he has always been loved and wanted things should be fine.
Why are you asking questions you already have an answer for? I know you already know. You are just looking for assurance that you might be right.