Akagi and Kaga were originally found in 2019. Akagi "only" suffered one direct hit. She also suffered from a very close near-miss near her stern, which damaged her steering gear. But that one hit sufficed to caused an uncontrollable fire, which cooked off munitions. Kaga, on the hand, got pummeled and was a burnt out hulk when she finally was sunk.
Akagi and Kaga were a converted (during construction) battle cruiser and battleship, respectively. They pretty much experimented with aircraft carrier possibilities and tactics, were where aircraft handling and servicing processes were prototyped and developed, and were the first Japanese carriers large enough to be fully useful in WW2. Being almost literally the first Japanese carriers, they had design and process issues/flaws. Their hangars were enclosed, which is nice in bad weather, but meant that the force an explosion in a hangar would be confined to within the hangar. Such an explosion would take out most damage control people stationed there, and would almost certainly damage the fire main ... fire main, singular. The enclosed hangars also meant a damaged plane could not be pushed overboard out the side. In the Imperial Japanese Navy, damage control was handled by specialists, with other personnel not being trained in damage control.
At Midway, US bombs penetrated into and exploded in hangars filled with fueled and armed planes and other ordnance in temporary holding cradles. Damage control people were stationed in the hangars. Thus, most damage control specialists, plane mechanics and technicians, and plane handlers got wiped out, the fire control mains breach, with no redundancy to permit re-routing, and fuel leaked out and set afire. With no ability to control fires, the cooking off of bombs and torpedoes was a matter of time. Akagi, Kaga, Soryu, and Hiryu had glass jaws and USN dive bombers shattered them.
