A natural armour bonus improves armor class resulting from a creature’s naturally tough hide.
and, from the Incorporeal monster rule
An incorporeal creature has no physical body.
An incorporeal creature’s attacks pass through (ignore) natural armor, armor, and shields, although deflection bonuses and force effects (such as mage armor) work normally against it.
My understanding is that, since the Smokeshade has no body, it has no hide to be naturally tough. Therefore, it should not add the natural armour bonus from the familiar table. Exactly as PlutoThePlanet stated in his comment.
Having no natural armour, it would not get any bonuses from Barkskin either.
Furthermore, being Incorporeal has more advantages that easily fill the gap from this "lost AC", so arguably, you wouldn't miss it:
It is immune to all nonmagical attack forms. Even when hit by spells or magic weapons, it takes only half damage from a corporeal source (except for channel energy).
Lastly, if you still feel that your (or your player's) familiar is missing out on the extra AC, I would discuss the possibility of adding half that bonus as extra deflection bonus. But this last option is just my opinion, and I haven't tested this scenario in any way.