I understand both sides of the coin. I personally would say for RP/realism reasons, the bark shouldn't count as armor. But for the game mechanics, I'd say it should.
Ergo, this is a place where I believe game mechanics weigh out over the RP/realism in order to make the game more enjoyable for all. I think a barkskinned Dryad would give much more to the atmosphere than one with brown makeup wearing a leather jerkin. Besides, if someone builds a wooden suit that looks good, they should get the points simply because of the effort put into it. Of course, that would then mean if someone wore a fur suit for a wyldkin, he should get the Armor points for it too.