This regards Nagumo's withdrawal.
Probably the single best vetting of this contrived issue is found in Willmott.
The single most damning indictment of the idea of a third strike was timing. Launching a third strike the same day would have necessitated a night recovery, something for which every single one of the Japanese carrier aviators was technically "out of qual" for due to not flying any night approaches or landings in at least two weeks. Some parties love to jump up and down about how well trained the Japanese aviators were, but I suspect not one of them has a night trap in their log books. I came within three of equalizing my day and night traps and night carrier landings are not a trivial issue...especially on an axial deck, in pitching seas, tired from flying a second five-hour combat mission. Launching a third strike the following day would have put the destroyers in extremis for fuel, and potentially expose the carrier force to all manner of retaliation from air, surface and below.
The next limiting issue was the aircraft available and the damage done to them. Only 29 aircraft were shot down, but another 111+ were damaged (and at least 20 of those were deemed constructive total losses). From the first wave, 8+ torpedo-armed B5Ns were damaged, and 10 AP bomb-armed B5Ns, and 17 D3As. From the second wave, 16 B5Ns, and 41+ D3As were damaged.
Looking at these figures, as well as the loss of 5 B5N torpedo-carriers and 14 D3As, Genda concluded that the environment had become unsurvivable for B5Ns and made the decision not to include them in any follow-up strike under consideration. Then they looked at the available D3As. Of those, the majority had just landed and still needed to armed and fueled, and in 58 cases, they needed to be repaired to some degree. So all that remained available was 56 undamaged D3As, 23 of which had just recovered, and only 33 of which could be made immediately ready. Unfortunately, those 33 had recovered in the first recovery and were in the deepest recesses of the hangars, farthest from the lifts.
So if there was going to be a third strike the same day, it was going to be D3As and fighters. Unfortunately, there was a premium on both types due to the need for a CAP in the event of retaliation either from the island, or from the missing carriers. In the event the missing carriers appeared, an anti-shipping strike would desperately require D3As to knock out those carriers. Since the carriers were not in the harbor, one of the first priorities for the Japanese carriers had to be organizing an anti-shipping strike as a contingency.
Thus a third strike the same day wasn't going to fly for aircraft availability, and of course it wasn't going to fly the next day due to the destroyers' fuel state.
The final issue is one of just what took place on Akagi's bridge regarding the discussion of a third strike. Pertinent to this issue are Yamamoto's orders to Nagumo which nowhere specified the base facilities as targets. Nor did Yamamoto's orders specify anything about a third strike. The orders Nagumo issued raised the idea of a third strike as a concession to Genda. The mission objective was to sink or cripple at least four battleships and delay the United States from interfering with the Southern Advance for at least six months. Nagumo could definitively say that he had met his mission objective and then some. And despite some fantastic contingency plans by Genda that contemplated loitering for unrealistic periods (something impossible due to fuel), after Genda decided it wasn't safe for B5Ns over the target due to the mounting AA fire, those contingencies looked fanciful at best. Genda did not press the idea of a third strike when the time came. Fuchida claims to have pressed the issue when he landed, but Fuchida lied. The conversation he recounts actually took place a couple of days later and was rather wistful. Both Genda and Kusaka exposed Fuchida's lie long ago in Japanese language accounts that most Americans are unfamiliar with. Kusaka and Genda also exposed that although Nagumo included his concession to Genda in the orders he issued, he had no intention to following through on that concession. Genda reported that beforehand his representation for a third strike was "should the first [two] fall short" which they most certainly didn't.
Another issue that is not addressed by Willmott, is the suitability of ordnance available to some of the suggested targets. The drydocks were virtually impervious to the available weaponry. The shallow water torpedoes were expended, as were the AP bombs. What remained lacked the necessary characteristics to effect heavy concrete structures. As for the tools and dies in the machine shops of the Navy Yard, they probably would have survived any bombing, even if the buildings house them did not. This was the common experience in Europe with similar facilities raided by heavy bombers dropping more and larger bombs, so such an attack might not have produced the desired results and Hawaii is not exactly an unpleasant environment to work outside. The oil tanks were certainly flammable, but not necessarily easy to hit, ignite, or spill, and the majority were diked to prevent run-off into the harbor.
Losing these facilities and supplies even temporarily would certainly have been a blow, but not as fatal as many officers' later hyperbole implies. More-or-less permanent shop buildings don't take long to erect, not do oil tankers. Filling them would certainly take a few months, but that too was well within American capabilities. However, the likely result of a third raid on this facilities would be much less than total destruction. Dive bombers are fairly precise, but a dive bomber pilot can't tell where to plant his bomb in a building to score the direct hit usually necessary to destroy machine tools and dies. Hitting oil tanks could certainly set them afire, but only breaching their sides will really get them to spill their contents and such a hit is harder to achieve than simply putting a bomb through the top. If the tank doesn't spill, it can be extinguished, repairs and some volume of unburned fuel might be salvaged. Of course, precise hits are harder to make when under heavy fire, and the Japanese judged the fire during the second raid to be the heaviest they had ever encountered. This is a telling point because the Army batteries never got into the fight. Any third raid would also have that fire to deal with, in addition to the Navy's batteries, and any aircraft that could rise to oppose the attack (as some did to oppose the second).
The third raid was never seriously practicable or seriously considered. Yamamoto did not include the proposed targets of such a raid in his orders to Nagumo. Nagumo entertained a third raid in the orders he issued to humor Genda, who suggested such a thing only in the event the earlier raids failed in their objective. Genda entertained other contingencies, but those contingencies were impractical and he never pressed for any of them with Nagumo. Nagumo and his Chief-of-Staff, Kusaka, looked at the situation beforehand and came to the basic conclusion that a third raid was impractical and had essentially already made the decision against it the night before, something of which Genda was aware. Fuchida's self-reported remonstrances of the day, were, in fact, wistful discussion of might-have-beens a couple of days later.