OK, so let's say Lexington and Yorktown are at Pearl Harbor. Does that mean that KB delayed their attack by 24 hours? If yes, doesn't that perhaps change the alert status?
Nevertheless, if everybody is home. Lexington is moored on the NW side of Ford Island, behind Utah and Enterprise is moored where Neosho was OTL (between California and Oklahoma), sitting at an angle to the battleships. This was their usual mooring spot when in port.
Lt. Nagai's force of 16 torpedo planes were designated for the carrier attack and he is approaching from the WNW (directly into the sun). 2 of 6 torpedoes launched at Utah hit the target (1 of the misses hit Raleigh), which shows the problems caused by attacking into the rising sun. So, let's say Fuchida recognizes the carriers early and notifies Nagai to attack carriers. I assume he would attack Lexington with 8 aircraft and loop the other 8 around to the south to attack Enterprise.
Overall, I believe the torpedo hit rate was 50% (including misses that hit another ship). Have seen a report that only 33% hit the target they were aimed at, but I think that is low. They apparently launched at the two easiest targets to find on their approach, In any event, from Fuchida's after action report, it looks like 12 of 21 (57%) torpedoes launched at Oklahoma and West Virginia were hits. So, perhaps reasonable to conclude that the probability of a hit was better for aircraft attacking from the East, especially those flying up the Southeast Loch. However, Fuchida knew all along that pilot skill was always a factor in their testing and rehearsals (as expected). I would just note that OTL, part of the Nagai group flying around the South end of Ford Island attacked up the main channel and launched torpedoes at Oglala (mistaken for a BB) and obtained 1 of 5 hits (20%), a torpedo passing under the Oglala hit the Helena. Interesting that the 57% hit rate was the Murata force, while the two attacks attributed to the Nagai force had success rates of 33% and 20% respectively.
Because of the angle of her berth, attacking Enterprise requires assembly over Hickam Field and an approach over the Navy yard which is less than ideal, and probably requires a higher angle of attack. If they approach up the SE Loch and veer left, they do not have a beam-on shot. Not a good percentage approach for the Nagai group, which was not all that successful OTL. Bigger targets in this scenario, but does the Nagai force do significantly better against the carrier targets than OTL? If so, by how much? I would guess that 3-4 torpedo hits on each would put them on the bottom (in about 40' of water). So let's say they get sunk.
Does Fuchida change the attack plan due to the presence of the carriers? I doubt it, because the attack plan already had that contingency and allocated 16 torpedo planes to the carriers. He does have 36 dive bombers with 250 kg general purpose bombs in the second wave allocated to shipping targets. He would probably allocate some number of those to the carriers for sure. How destructive would they be and what would their hit rate be? Enterprise is certainly going to be shrouded in smoke.
Does this necessitate the 3rd strike? It is my understanding that Fuchida and Genda wanted it in the first place, but do they get it? If Nagumo now knew where the carriers were at Pearl Harbor does he relent? And, if so, how much of the smaller 3rd wave is allocated to shipping versus infrastructure? Even if, I do not buy the premise that the Fuel farm is lost for a year. The article referenced talks about replenishment oilers, not the tankers used to supply PH (reasonable mistake for a USAF officer). Operational reach is a different issue than the ability to rebuild and resupply a fuel depot at PH.
IMHO, it is hard to imagine the US would not make a significant effort to salvage the carriers. I would bet it receives their highest priority. Are they un-repairable? I do not think that is clear at all even though some have declared that would be the case. The aircraft on board would not be fueled in port, so no raging gasoline fires. 500lb GP bombs are not that destructive, and while many label the wooden-decked US carriers as having the proverbial glass jaw, the fact is that their hanger deck is their strength deck. As a result, the GP bombs are not likely to penetrate into the engineering spaces or magazines.
What is the effect on the war? Not as much as one might think even if the carriers can not be repaired. The Pacific Fleet would probably have three carriers available for Midway in any event (assuming it still happens). Port Moresby probably falls and perhaps there is no US attack on Guadalcanal. This really does not change much, and in my opinion if the Japanese want to expand further during this carrier gap, "be my guest". They have already exceeded their logistical reach, so placing more troops in more distant places only makes things more difficult for them in the long run.
Regardless of the 3rd wave or carriers, the Japanese accomplished their goal (which was simply to prevent the US fleet from attacking the flank of their Southern operations). The fact that it wasn't going to happen in any event being irrelevant.
Even if Moresby falls, does that prevent US troops and supplies from reaching Australia? No!
Does that prevent the flow of supplies to the DEI? No, it was already impossible.
Midway? Why would Yamamoto not be even more bold? Pacific fleet would have 3 carriers before that date. Not sure how this battle goes away.
Does that prevent the US from attacking Westward in 1942? First, they didn't have much reach to begin with so the major offensive crossed off the list is Guadalcanal, and should make the Doolittle raid too risky. What about Kwajalein? That actually fits better with Navy plans anyway and scratches the "do something" itch; and it is within range of the West Coast.