Complex sentence: The alternative explanation is that the bomb penetrated the armored decks and detonated directly inside one of the starboard magazines for the main armament, but smokeless powder is relatively difficult to detonate and the 14-inch powder bags required a black powder pad to ignite the powder.
Split into simpler sentences: The alternative explanation is that the bomb penetrated the armored decks and detonated directly inside one of the starboard magazines for the main armament, but smokeless powder is relatively difficult to detonate. Thus the 14-inch powder bags required a black powder pad to quickly ignite the powder.