Possibly the "weakness" of Shokaku and Zuikaku saved them as their sides blew out when hit (a "flaw" that also apparently saved US carriers from fatal damage), Akagi and Kaga (based off British Battlecruisers) died very easily. But i'm way beyond my knowledge here
P.S. fun fact, the picture of late war Japanese graveyard planes above, probably post surrender pile ups, contains many 13.2mm nose gun Zero's (larger vertical ejection port vs more horizontal small ejection port for 7.7mm). (fun fact #2, Zero changed from 0.30" to 0.50" almost same time as Spifire did mid'44!)
Purely from a war nerd viewpoint its disappointing the original 6 fleet IJN carriers didn't get to fight together again.