Cause the boomerang of normal Link is a ancient weapon of the forest. Some sort off boomerang of the wind.. and the hero of Hyrule which means normal link left, and then the tsunami came..
Toon links world is in the future where Hyrule got drowend into a big tsunami.. Toon link's boomerang is some toy..
Do you see a toy bringing a whole person to you? I think not.
That boomerang of normal Link is taken by himself, wherever he got to..
Seems they keep some things with the game/lore.