Seems you've already received an answer; but I'll actually explain it. There used to be an option to "lock" your subclass in place. That is to say, if you loved your class tree as it was you could hit the lock button and in doing so you would get bonus increases. I believe whichever one you chose would get put in that empty slot. That, orrrr it simply fits in the menu as every other item has three horizontal boxes. Orrr Bungie indeed has more subclasses hidden away. Hoping we do get some though.