A few thoughts about the PH strike from various sources. I think the most likely result would have been that the carriers would have been sunk if they were in the vicinity of PH. If in the harbor their planes would likely have contributed nothing to the defense since they would have been parked wing-tip to wing-tip on the USN airfields (probably with no gas and no bullets and certainly with no bombs or torpedoes).
If the carriers had been in port, they all would have been sunk or put out of action in the first strike.
I think that the majority of the dive bombers in the first strike were targeted against the airfields. The torpedo bombers and level bombers were targeted on the battleships. Flexibility in the execution of the plan of higher command was not a trait frequently demonstrated in combat by the Japanese during the war. The plan called for the dive bombers of the second wave to attack carriers and cruisers. The actual attack contradicts my previous comment somewhat because the dive bombers of the second wave actually concentrated on the USS Nevada instead of the cruisers they were supposed to hit. The pilots were aware that Yamamoto had placed a premium on sinking BBs and in the event they didn't have to make a choice between Nevada and Lexington or Enterprise so they deviated towards the prime target (one might argue that Lcdr Fuchida placed a higher priority on carriers but if one did one would have to place undue reliance on his post-war interviews and writings which have been widely discredited [especially in Japan]).{Zimm: Attack on Pearl Harbor; Strategy, Combat, Myths Deceptions}
The Japanese probably were flying some kind of search. The Tone and Chikuma were along with their large sea plane contingent. These two cruisers were designed to use their air group as air search for the KB.
The Japanese were not inclined to use any strike (B5 or D3) aircraft for searching. Tone and Chikuma were designed and intended to scout for the carriers BUT their combined complement of seaplanes was only barely able to carry out a search of around 120 degrees. Such a search was dangerously thin especially if one considers how such a doctrine turned out at Midway. Certainly no "super-search ability" was demonstrated in that fight by these two ships. (Parshall and Tully: Shattered Sword).
The KB retained 48 A6M2s for fleet defense. Roughly 1/3 to 1/2 would have been airborne at any one time. The KB had no radar, no Fighter Direction Center and in many a/c: no radios. An escorted strike coming in on an unanticipated axis might well have caused some serious damage to the KB. The USN was not practiced in multi-carrier strikes in 1941 and plane characteristics and inexperience certainly made an uncoordinated strike a good if not likely possibility. But then again Yorktown and Lexington put together good coordinated strikes both against Lae/Salamaua and the Shoho pretty much right out of the on deck circle so dismissing the USN's ability to do so against KB is not entirely justified. At Midway 1 x 1000 lb bomb killed Akagi.
I've experimented with turning 1st Turn Surprise and Historical 1st Turn OFF and then stuck the Japanese with doing just what they did in the way they did it whilest the Allies get to try any and all surprises against the IJN. I'm afraid that the results obtained seemed pretty much what the IJN would have wanted. I admit that any IJ Player who continued after any other result would have to be a real diehard masochist but after quite a few run throughs it seems the system will not permit any great disaster for the IJN. The real IJN Command considered this a really high-risk operation: in the game it's not