You don't have to worry about that discussion, because the Armour Class-system of D&D is ass-dumb anyway. It assumes that you actually try to hit the non-protected places, not trying to hit through the armour of the enemy. So, really, if you're fighting a monster with thick hide, you're not trying to pierce its skin, but hitting on vulnerable joints, or its eyes, the neck, anywhere where you approximately know that its not that well protected.
Unless playing with optional rules, armour doesn't give Damage Reduction, which would really be the logical way. But because of the AC-system, it doesn't (or wouldn't) matter if the monster with +8 Natural Hide Armour wears a chainmail. You wouldn't try to hit it in its stomach section anyway, but its head, or its foot, or something similarly inane.
That's how AC really works. The fact that D&D 3rd edition allowed the stackability of natural and worn armour while stating that fighting with the AC-system means you try to hit the non-protected area was just contradictionary crap... Natural AC and worn AC shouldn't have been able to stack at all by their definition, but the designers for 3rd edition didn't think that really through.