I've not posted on this thread thus far, but I've been following it with admiration for you OP.
The reason I am posting now is that, although I agree in the main with not communicating with your ex, when it comes to the subject of your son raised in the recent email, I disagree with advice here.
I agree that the response to his email should be business-like and to the point. But when it comes to the issue of 'making it up' to your son, I think it's for you to speak out here to explain how his actions have devastated your son. I think it needs to be expressed in a calm, objective, rational language - anything heated and impassioned he will dismiss as being motivated by your own bitterness - but I do think it needs to be said.
The reasons for this are as follows:
Your son is too young to be able to fully articulate to his father his feelings about his father's behaviour, and he may prefer to hide those feelings.
If you don't tell your ex exactly how his actions have impacted his son, he will never know, and he will be able to kid himself that actually what he did was fine, he can disappear with no word, and there were no major repercussions and it's all good. etc.
Leaving the family home with no warning, as he did, was just as much a betrayal of your son as you.
Your ex will want to be able to continue with your son as if nothing has happened, he will want your son to 'forgive' him & get back to normal asap, so that he can carry on without any guilt.
If your son were older he could articulate his anger, shock, disappointment, hurt, himself. But he's too young.
In summary I believe you should tell him, because if you don't, no-one will.
It's for you to explain that a father disappearing like that has consequences, that it was a betrayal, and that he has to take responsibility for those consequences.
I understand in posting this that others may not agree with me and that's fine. This is my personal opinion, this is what I would do, obviously, you are free to make your own choice.
Best of luck OP to you and your son.