Okay, you need to let go of your son having herpes from birth. If he had it, he would have been very sick, and you wouldn't have missed it. The doctors wouldn't have missed it. Your son would have been in the NICU and on special medications for it.
They did a vaginal birth because your wife didn't have an outbreak. Millions and millions of women with herpes give birth every year to healthy babies. Your wife is one of them. You need to let that go. It's not fair to your wife or your son.
Babies born with herpes don't just have it on their genitals or in their eyes - it's a full body infection.
The only way your son will get herpes from your wife now is if she has inappropriate sexual contact with him, if she even has herpes. To get it from you, he'd have to have the same inappropriate sexual contact. Let it go.
Herpes in the eye can happen, but it's not common and if you think you have it, you need to see an opthamologist. More likely, you have allergies or something that is causing red, watery eyes.
Your son - did he have phimosis? That's when the foreskin can't be pulled back. Betaderm is a common treatment for phimosis. Herpes has nothing to do with phimosis.
Does your wife even have herpes? Is this all just a big fear of yours? You don't know for sure if you do - do you get outbreaks? Can you get your doctor to do a type specific IgG blood test? It's harder to get them in Canada, but maybe your doctor will do it to help ease your mind.
Your son is fine. If you need counseling to let this go, get it.
HSV can be passed on but it is very very very rare. Itching in itself its not a good symptoms of herpes so be led by your doctors thinking. Something like allergies or hey fever is much more likely