They have stronger tendons, bones, and scales, scales that can vary in size. CNT is flexible, thus armor, made with it, can be too. So, I just eliminated the last practical reason for why dragons have soft underbellies and neck...
No, you haven't! Just because they have the metabolic pathways to produce CNTs doesn't mean they have the metabolic pathways to produce CNTs cheaply or efficiently. Armor that you don't absolutely need is a waste of energy to produce and maintain--and furthermore, even light armor is not weightless armor, so armor you don't need is just armor that makes it harder to fly.
So, do they actually need belly armor at all? Most predators don't actually have much armor. It isn't useful for them. Tigers, lions, wolves, bears, and so on rely on overwhelming force to take down prey before it has an opportunity to hurt them, and armor would only make it more difficult to chase down their prey. Most of the time, you find armor on creatures that need it to regularly defend from attacks, not on creatures doing the attacking. And dragons are so overwhelmingly powerful and dominating that it makes you wonder, why do they even have any armor at all? And why do they have it on the top and sides, when, y'know, they can fly?
The obvious solution, to me, is that they have armor not because it protects them from gallant knights--most of whom will never get close enough to land a blow in the first place--but to protect themselves from other dragons. If they are fighting another dragon on the ground, they can more easily keep their belly protected by just keeping it near the ground; and if they are fighting in the air, attacks coming from above are much more dangerous than attacks coming from below (where gravity would be working against the assailant). Thus, back armor makes sense--but belly armor remains largely pointless, and in fact is detrimental to any dragon who would have to fight with it in the air, where it would only slow them down, lower their flight ceiling, and make them less maneuverable.