So your son is witness to your AH's behavior, and then understands from his Dad that he is expected to keep the truth from you. Think about what he is learning as he grows up. Even if he does tell you, he is being played in the middle. He is learning manipulation first hand. Your AH doesn't lie, he just omits the truth? That IS lying. And this is all recent!
Follow your gut. It's telling you not to trust yet. So often we have a tendency to not listen to our guts, but it's a mistake.