To aid in penetrating battleship deck armor, the attack force at Pearl Harbor had dive bombers equipped with bombs that were modified from battleship armor-piercing shells. Dive bombers allow maximum accuracy with minimum time for the delivery vehicle within the AAA engagement envelope.
From this wiki chart of Japanese air dropped ordnance, it looks like the bombs were Type 99, Mk 80s, and thus ~800 kg, with around 30 kg of explosive filler, modified from 400mm naval artillery shells. The chart claims 150mm of armor penetration, which is nice, (and was certainly effective on the U.S.S. Arizona) but nowhere near the extent that a 400mm naval shell would penetrate in plunging fire. [Edit, and it looks like my Pearl Harbor point is already made. Need to type faster.]
It’s mentioned in the OP, but Iowa class BBs had by the middle of 1945, AAA emplacements that were probably a magnitude more effective than those of the Yamato, despite the latter’s giant (~160) number of manually operated 25mm AA guns. Yamato did not have radar guided 5in/38 DP guns like the Iowa. Nor did Yamato have proximity fuzes for its AAA. I am not familiar with the Iowa class’s record under massive air attack. I am slightly familiar with the closely related South Dakota BBs under air attack. During the battle of the Santa Cruz Islands in 1942, South Dakota alone accounted for 26 attacking planes during one day. Of course, the South Dakota was facing about a quarter of the airplanes that were attacking Yamato…
Finally, Japanese damage control was not noted for being a high priority in the IJN, nor was especially effective. Their most ignominuous failure being perhaps the loss of the CV Taiho from a single torpedo hit. Contrast that to the great emphasis placed on damage control by the U.S. Navy. U.S.S. Franklin is one amazing example; there are others from WW2.
I agree with the previous posters that if you throw multiple waves of 280 carrier aircraft at a WW2 surface combatant, said surface combatant is going to be sunk. I just want to state that I think the Iowa is going to take quite a few more planes down with it, and be combat effective for longer, despite having less armor than the Yamato.
Akin to what Elendil’s Heir wrote, 12,000 lb Tallboy bombs (the precursor to the 22,000 lb Grand Slam’s) were used in killing the German BB Tirpitz. The linked wiki for Tirpitz goes into much more detail about the effectiveness of Tallboy vs BB armor.