From a bird’s-eye view, Bomb Island does indeed resemble a bomb. It’s circular, with a narrow, curved path winding to the northeast that looks like a fuse from above. One of the three Traveling Merchants appears on Bomb Island after you begin the trading quest at Windfall Island (D2).
Empty Bottle #2 (via Submarine)
The submarine in this sector has a handy Empty Bottle. Sail to the submarine, then climb onto it and enter the doorway leading inside.
Face three Bokoblins and a few Rats. Defeat the Bokoblins to reveal a chest on the ground containing an Empty Bottle. You don’t have to defeat all the Rats to reveal the chest, but they’ll steal your Rupees if you don’t watch out for them!
Sea Platform
Sail to the single Sea Platform and climb its ladder. Defeat the enemies to reveal a chest, which contains a minor reward.
Piece of Heart #24 (via Secret Cave)
If you’ve found the Bombs item, you can use a bomb to destroy the large boulder on top of Bomb Island, revealing a hole. Drop into the hole to enter a lava-filled Secret Cave.
This Secret Cave is made up of two rooms. In the first, unseal the north door by stunning a nearby Magtail. Pick it up and place it on the pressure switch on the floor. To stun a Magtail, wait until it’s about to strike at you and then attack it with 
. The Magtail curls into a ball.
With the door unsealed, proceed into the next room. This second room is similar to the first, but much more dangerous. Walk down the extremely narrow pathway to the door’s left, taking care not to fall into any lava. Step on the switch at the end. Two rings of fire that were blocking the north pathway disappear.
Carefully make your way back along the narrow pathway. With the fire extinguished, you can proceed up the second pathway to the north. This takes you to a wider area, where two more Magtails crawl about. Each side of the area has a ring of fire, and a short distance up a pathway to the north is a chest surrounded by fire.
Stun either Magtail, pick it up, and throw it into one of the two rings of fire. It may take a few tries before the Magtail lands on the switch in the center. Repeat this process with the other ring of fire. Once you’ve activated both switches, the fires vanish, allowing you to reach the chest to the north. Open the chest to collect Piece of Heart #24.
Piece of Heart #39 (via Treasure Chart #20)
Find and open Treasure Chart #20 (found inside the Earth Temple dungeon at Headstone Island [C7]) to pull a chest from the Great Sea near Bomb Island. The chest contains Piece of Heart #39.