If he plans to come back to Thailand get his Thai passport sorted before you leave for the UK. You'll need to bring his birth certificate to the airport to show he was born in Thailand (hence no entry stamp).
The very first thing you need to do is get your UK Marriage certificate legalised by the UK Legalisation Office in Milton Keynes and then certified by the Thai Embassy in London. It's much easier to do this while you're in the UK. I'm sure someone else will advise you about the procedure once you're in Thailand.
I had always assumed that as kids were exempt from fines for visa overstays, the same would apply to fines for not doing 90-day reporting. Anyway, I guess the worst that can happen is it will be brought up at one extension and Dad will have to pay 2,000 baht!
How old is your son? Mine has lived here all his life on an O visa extension as my dependent and has never done a 90 day report (he's nearly 8). It's never been mentioned or been an issue when getting a new extension. I do mine and my wife's online.
An IDP is just a translation of your national licence. I don't believe it includes a Thai translation! That said, the police don't care and are looking for a reason to fine people.