Not necessarily. In 3.5, the Amulet of Natural Armor and the Barkskin spell don't provide a natural armor bonus; they increase the creature's existing armor bonus.
If you had a spell or an item that provided a +2 natural armor bonus, say (rather than increasing an existing natural armor bonus by +2), it wouldn't stack with the +5 he already has.
In a way, Barkskin and the Amulet in 3.5 work like an enhancement bonus on a suit of armor - the enhancement bonus increases the armor bonus of the suit, rather than increasing your AC directly. The Amulet increases your natural armor bonus, rather than increasing your AC directly.