I think the "problem" with their Armour class stems a bit from the nature of Dungeons and Dragons and how things work there.
We have to take 2 things into consideration there
- How do armor bonuses work?
- For what type of character is the vampire planed as an adversary?
Type of character
Vampires are meant to be adversaries for medium to high level parties. In Dungeons and Dragons this means they NEED a strong armor class in order to not be automatically hit by virtually any attack.
In the later Dungeons and Dragons editions like D20 there were rules for how to convert a normal person into a vampire. Now instead of just saying "ok this is that armor class live with it" they needed a general rule there and added an armor bonus of +6. Although this armour bonus should NOT be confused with the armor bonus gained through the dexterity bonus (as that is in addition so they gain +6 natural armor and +2 armor through the higher dex).
How does armor work?
As we saw before they needed an armor bonus in order to make them feasible as adversaries for high level parties. If you look at the armor rules you will find that there are plenty of armor bonuses that can apply....but each and every does not stack with its own kind (only with others).
More logical from an out of universe context would have been a profane modifier to armor as vampires are inherently evil and chaotic and thus a bonus from "powers of evil" would make sense there. But they choose the natural armor bonus.
So what is it?
A natural armor bonus improves Armor Class resulting from a creature's
naturally tough hide.
Now as we know vampires don't have diamond hard skill as else staking them would be quite impossible as a feat to do. But still they get a tough hide bonus.
The only possible explanation there (aside from an overlook by the creators of the vampire rules) is that they took a few things into consideration and thus decided on a natural armor bonus there:
- Vampires are undead: Thus they are more resiliant to damage than other beings. Although also skeletons and zombies are undead too this should not affect them too much.
- Vampire powers: In addition to being unliving and thus unbleeding vampires have fast healing and a damage reduction. If we take this into account you COULD see it that weapons (aside from silver and magic normally) just have almost no to no effect on a vampire at all. And also he regenerates most of the minor hits at once.
Thus as armor class itself also represents how hard you are to hurt this could be an ingame reason for why vampires have a higher armor class than their normal counterpart. In addition to this this is a natural part of being a vampire not an evil induced, not a luck induced, not given by a god, .... it is just part of being a vampire, part of its nature. Thus this could be a reason why they ruled that it is a natural armor bonus.
- Other types of armor class bonuses. If you look at them there is only one that represents general toughness that is not induced by gods,... and that is in addition not just you evading the attack but instead taking it, smiling and hitting back. That is th enatural armor bonus. Even though it says about tough skin there it is the only armor bonus that represents pure and other toughness.
So in total the natural armor bonus is not the best fit (in terms of fluff text for the armor bonuses) BUT it is the only fit that stands for what the vampire designers wanted to portray, that the vampire just can stand up to you, take a blow (by you missing the AC bonus) and smile while you see not a single effect there on him. Although this is redundant with the damage reduction (and beats it as the damage reduction is of no use against silver or magic) it would fit in with what is being portayed there. In addition to it with the available types of armor bonuses it is the best fit there ruleswise and what can be portrayed by which armor bonus.
As of note. The stats I talk about (and also rules) are mostly from the 3.5 and d20 versions (the D20 version can be found at: http://www.d20srd.org/srd/monsters/vampire.htm). In later versions like d&d 4 these things change though. Like in D&D the vampires gaining a shield bonus instead of a natural armor class bonus.