I assumed some of them were just available, and they just choose to equip it or not. Kirito did say something in one of the episodes about the Hearing skill, something along the lines of,

"You can listen through doors without knocking with a high enough Hearing skill. It is just that almost no-body bothers to level it up."
I was under the impression this meant, everyone has the Hearing skill, but only some bother to equip it and level it up.