New Info on Getting Super Bomb in the Dark World Bomb Shop
In addition to completing the Ice Palace and Misery Mire, you also need to acquire the Tempered Sword (Lv 3) from the Blacksmiths. The Super Bomb will not show up in the Dark World Bomb Shop until you do so. I've recently played The Legend of Zelda: A Link to the Past and beat it with the least amount of items and equipment as possible; and considering the Master Sword does zero damage to Ganon, you need to have at least the Tempered Sword.
Additional Info on Super Bomb Requirements
The Tempered Sword is not required for the Super Bomb to appear in the Bomb Shop, however, rescuing the Blacksmith is. The developers made this requirement because of hardware limitations preventing more than one character/item to be following Link at any given time. Furthermore, the Master Sword can damage Ganon only by using a spin attack. Also, if Link does not get the Tempered Sword from the Blacksmiths and throws the Master Sword into the Fairy Fountain in the Pyramid of Power, he will receive the Tempered Sword in return. ~Blake