Shortcut #1: Goron city to Lost woods
Light with lit deku stick or throw bomb flowers to bomb rocks and way will be revealed. (Tunnel on second floor in Goron city lost woods head right from entrance then left and then straight ahead.)
Shortcut #2: Zoras river to Lost woods
Win silver scale and pool of water with hole in connecting can now dive into. (Zoras river it is right of Zoras Domain entrance and Lost Woods it is from entrance right left right and then straight ahead.)
Shortcut #3: Zoras Domain to Lake Hylia
Win Silver scale then can now dive into connecting hole. (Zoras Domain it is in water straight ahead after diving down waterfall and Lake Hylia it is in water straight ahead from scarecrows then turn around and look in wall.) Note: Only accessible as child since Zoras Domain frozen as adult.