I don't bother doing 90 day reporting for my 3 year old son, although I do it for myself and my wife. Immigration have never said anything or suggested I should be doing it for him (he and my wife have Extensions piggy-backing on my work Extension). I doubt he could be fined anyway.
If he's never left Thailand, does he have a passport? If not, he can't have a visa. Tod Daniels will correct me if I'm wrong, but once he needs to leave the country, you take his Thai birth certificate with his passport to the airport and he will get an exit stamp and a note in his passport that he was born here. When/If he comes back he will need a visa. How long a non-Thai person, born in Thailand, can remain here without ever leaving, I have no idea.