Unlike OOT3D, the hookshot in MM3D cannot simply clip through walls by strafing against them. Instead you will need to position a hookshotable object against a wall, and sidehop into the object releasing hookshot right as you hit the ground. Keep holding L until you've successfully clipped throug This can be used to clip into the Music Box House as seen below, and to skip the Boss Key fight in Woodfall Temple.
If you do the Text Storage RI as Goron and use the hookshot next to a wall, Goron link's arm extends out enough to clip the hookshot through the wall. It is now replaced by EHS.
Bow clipping can still be done the same way as OoT3D. Simply face parallel to a wall and be up against it, then hold the control stick perpendicularly into the wall and mash L a few times as fast as you can, then release L, and aim into the wall and shoot. This currently does not have many uses, however it can be used to spawn a chest early in Stone Tower Temple.