T2, I think you need to find some time and have a nice chat w/your wife about your son's concern about letting her know when he's ill. There is absolutely nothing wrong in sharing w/her what your little one said.
She's far enough along now to hear some of these things and she needs to be aware that her child is hesitant to approach her when he's not feeling well.
She needs to hear this and soon.
Sit quietly, the answers will reveal themselves when you least expect them to. The past is gone, the present is a gift and you need to focus on today, allow the future to reveal itself when it is ready.