In-game evidence please.
The encyclopedia can say what they want, as long as it's not said in the game, it doesn't have to be true. This pendant doesn't look the least bit like wood to me, save for the string. Seriously, that pendant is not made of wood.
Edit: Now that I read carefully, like you should've probably done also, it says enigmatic pouch and wooden pendant. I guess they mean with this the amulet is a pouch, and the string is made from wood.