It applies even when armored, as it's a bonus, not a different way to calculate AC
While page 276 implies that Natural Armour is in lieu of AC gained from manufactured armour, Natural Armour grants you a numeric bonus to AC, not a new way to calculate it. Relevant quote:
A monster that doesn't wear armour might have natural armour, in which case it has an AC equal to 10 + its Dexterity Modifier + its natural armour bonus
While this does strongly imply that Natural Armour is a new calculation, I would like to refer you to the Monster Manual, specifically the section on players being cursed with lycanthropy. If we look at the werewolf specifically, it says this (emphasis mine):
The character gains a strength of 15 if his or her score isn't already higher, and a +1 bonus to AC while in wolf or hybrid form (from natural armour)...
Neither the section on Natural Armour nor the section on player lycanthropes say that you do not gain this bonus when wearing armour. The Natural Armour section implies it, but it does say that Natural Armour is a Natural Armour Bonus, implying that it would stack.
Seeing as nothing explicitly forbids the use of armour with your natural armour bonus, and Natural Armour is described as a Natural Armour Bonus with a value typically in the range of +1 to +3, we can add our Natural Armour Bonus to our Armour Class.
You could argue that Natural Armour changes your unarmoured AC calculation, but examples from the Player's Handbook all specifically say that they alter your unarmoured AC calculation if they don't grant a bonus. This again implies that Natural Armour stacks with manufactured armour.