To use other weapons on Epona, you need to get rid of the Master Sword. One way of doing this is in the second battle of Ganon. When he knocks the sword away from you, save it, and press reset.
Now open the saved file and don't equip any swords. The green button should be blank.
Go to Hyrule Field and play Epona's song to get Epona. Now press different C buttons to use the items. You can use Deku Nuts to get off the horse and walk on foot and control the horse at the same time. You can also use the hookshot if you want the game to lock up.
NOTE : You won't lose the Master Sword by doing this. Any time you want it back to normal, equip a sword or go back in time.