Edit - just noticed now, after posting, that I'm replying to very old posts.
What the heck else are they going to have been doing?
If the Kido Butai hadn't been preparing a strike when the US carrier aircraft came over the horizon, they'd have been complete fools because - given the timings through the course of the day - to not have a strike available, to not have fuelled up aircraft at the time of the US carrier attack, would mean they'd have not even begun to prepare a strike for the entire day after the Midway strike.
Doctrinally, what Nagumo needed at Midway was some sort of rapid-fire strike doctrine where each carrier launched small waves (6-9 bombers) every half hour or so. Trying to arm all the bombers on all the carriers for some grand strike when the US carriers were known to be aware of Nagumo's position by 0500, and the strike could not depart before 1030 was starkly incompetent - it gave the US carrier
five and a half hours to deliver the dive bomber strikes that end Kido Butai.
The numbers just don't work out. The only time slot they could have spent in spotting and launching a strike - any strike - that day is the time slot when they were recovering the Midway strike.
That's simply not correct, IMO. Hiryu was under torpedo attack from 1015 to 1040 and launched at 1054. TB-3 simply did not slow Hiryu's strike preparations down by much - it forced the carrier to run with the wind until the threat was clear. But torpedo bombers could not prevent carriers from spotting and warming up, and the actual launch was only a few minutes, meaning that at most the strike would have launched over the course of a half an hour from the multiple carriers and then assembled and departed.
If they'd done the launch then instead, it would have meant abandoning a good hundred or more aircraft - cutting their strike power neatly in half.
Fuchida's B5N2 launched at 0600 for Pearl Harbor and didn't recover till about 12 or 1pm - six to seven hours in the air. The Midway strike launched at 0400 and was back by 0800 - four hours. It is possible that some of the Midway Strike - some of the damaged aircraft - might have ditched. But certainly not the entire strike.
(All other time slots were interrupted by American air strikes, and usually by the need to send up more fighters.)
https://upload.wikimedia.org/wikipe....jpg/1280px-Kaga_and_Zuikaku_Pearl_Harbor.jpg
Looks to me like a picture of Kaga with a large deck park aft and two ready Zeros spotted forward ready for launch.
So, there's either going to be fuelled aircraft on the Japanese carriers below-decks at the time of the US dive bomber strike, or the Japanese have decided that they will not be attacking anyone today.
Yamaguchi should have either counterattacked without orders, or broken radio silence and contacted Yamamoto, who would have ordered him to attack immediately at 0830.