You can more than easily restock on the more important stuff, such as arrows and bombs by breaking random crates or vases or by slashing grass anywhere in Termina.
However, if you want a reliable (and still easy) way to restock, you can always try to get the two silver ruppees in Clocktown to buy what you need from the Trading Post or the Bomb Shop.
The two silver ruppees can be found at the following locations:
East Clocktown: Starting at the entrance to the secret passage to the Observatory, go directly south, up the stairs, then jump over the platforms until you have no other choice but to go right (West). The ruppee is in a chest.
Secret passage to the Observatory: When you reach the waterway, go left (instead of right). You'll notice cracks on the wall: Use the Bomb Mask or a bomb (if you have one) to reveal the chest in which to find the ruppee. If you use the Bomb Mask, you can explode without suffering damage by brandishing your shield while exploding (R + B).
Those chests will always contain a silver ruppee every time you start a new cycle, and are therefore a great way to farm ruppees safely.
Using the following map, the two chests are denoted by a green
5 and a green