Yes, I went through this as well. My son has weaker enamel and etc. than his sisters (who never had a cavity)....plus his dad was sneaking him the bottle at bedtime when I was at work in the evenings! I was so upset when I found out (and furious with my husband).
I think the big concerns are managing their anxiety. Luckily your son is old enough to talk things over with. You can talk about how he needs to have his teeth "fixed" so that he doesn't become very, very sick and so that his mouth doesn't start hurting a lot. Talk about how the dentist is going to help him, really build it up as a good thing in this respect.
And talk in a brief, calm way about how you will stay there at the office the whole time and be there for him when he's all done. If your dentist won't let you stay in the room with your son, be sure he knows that, but explain why you can't be in there. Try to frame it in a positive way.
And you can plan together how you will share special time together afterwards. Maybe rent a special movie and cuddle together. Or play a favorite game together.
We did this with my son when he had to go back a year later for follow up work and these things seemed to help him. I really emphasized how this was something we had to take care of, to prevent worse problems down the road. We even joked together about how he if we didn't take care of his teeth he wouldn't have any left and then how would he eat his favorite foods.
And we talked about how he was nervous/scared. We talked about times he had been brave and about what a big boy he was and all the things he could do. And I told him that I knew he could do this too. And about how it would only last a little while and then it would be all better. And then I asked him if he could think of something we could do after the dentist that would make him really really happy. And he picked a special toy he had really been wanting.
And so when we went in for the precedure, we reviewed how great he was going to do and how we would go to the toy store later. And we talked about the thing he wanted (a $10 toy) and what he would do with it.
And he did great! It had been so traumatic for both of us when he was 2 1/2 but at 3 1/2 it was a breeze by comparison. When he came out I asked him how it went and he admitted he'd been really scared. I told him I understood, that I would have been scared too if I was him. But I pointed out that he'd done it anyway. And now his teeth were fixed. And I told him that's what being brave is-- doing what has to be done, when you're scared. And I told him he was a really brave guy.
He shed a few tears and hugged me. And I could tell he was really really proud. And later we went to the toy store. And of course I made a point of telling the family, in front of him, how well he'd done.
So just talk to the dentist and find out what to expect -- if you can stay with your son or not, how long it will take, etc. And just make sure to keep yourself calm-- or have your husband go if you get too emotional. Because the kids get more scared if they see us scared.
You can also ask the dentist what medications they will be using, and about the chances of an allergic reaction. When my son went the first time he he broke out in really bad hives and swelling afterwards, a reaction to the meds. So thereafter they used a different one, and no problems.
Also, I was tweaked out about him not having his top front teeth. But once they were out... I realized he didn't look "wierd", he just looked cute! And when he went back to nursery school... no one even noticed. Hard to believe but true.