Oracle Placement In Zelda Timeline

[Koopaul]

This is a decedent of the original Link. Aonuma/ Miyamoto said that this takes place 100 something years after OoT. Seeing how the Kokiri were a small band of children that relied on the Deku Tree, I wouldn't be surprised if they all died out.

Either way, some things do make sense. If you remember, as an Adult, Ganondorf killed all the Zoras (except Ruto, the King, and a shop dealer) which is why there are no Zoras in the Wind Waker but there are still Gorons because Link managed to rescue them.

But Twilight Princess did have Zoras because Ganon's reign of terror never occurred.

Just because things seem unclear to you doesn't mean there isn't a timeline.