This point cannot be overemphasized, because from the conventional belief of what was on the flight decks flow nearly all Western interpretations of the battle.
Before the days of modern angled flight decks, a carrier flight deck could be doing only one of three things: spotting aircraft, launching aircraft, or recovering aircraft.
The conventional wisdom has always been that when Lieutenant Joichi Tomonaga's Midway attack force was launched, the reserve antiship strike force was immediately brought up to the flight decks and spotted.
75), "It should thus be apparent that if the rearming operation was reversed at this point--at 0745--it would not have taken much time to restore the torpedoes on half the planes from which they had been removed and respot all the planes on the flight decks of the two carriers, perhaps only about thirty minutes." In light of the need for forty minutes just to respot the strike, not to mention the time needed to rearm, this gives a grossly optimistic impression of Nagumo's chances of launching a strike before Tomonaga's returning force would begin to occupy the flight decks at 0837.
77), "Thus, at about 0920 operations to respot the second-wave strike force on the flight decks could have begun, had the torpedo planes been rearmed with torpedoes.
The torpedo planes that had been rearmed were brought up to the flight decks, beginning around 0920, but at least a third remained in the hangar decks at 1000.
Considering this, Nagumo probably thought he was playing it safe--keeping the strike aircraft in the hangars until the worst of the danger was past, keeping the flight decks clear to support constant CAP operations, and repelling American attacks with the best weapon available, his fighters.
It is also important to bear in mind that he was laboring under the conventional belief that the second-wave strike was spotted and ready to launch on the flight decks, rather than below in the hangars.
In order to spot a strike force on the flight deck and launch it against the Americans (assuming it was already armed), Nagumo's ships had to perform a complex series of operations.
* Bringing the aircraft up to the flight deck (sequential: approximately one minute per plane).