I don´t think you got all you facts straight. The Japanese carriers were not working alone, there were multiple destroyers and cruisers around, they are just giving space for the carriers to manuever to dodge torpedos and bombs. Also the planes onboard were refueled and rearmed below deck, so no planes would be visble on top of it whlst that was going on, it did most definitely have an impact on the sinking of the carriers. Thirdly only the 3rd wave of American planes scored hits, whilst the first 2 waves were lost with all hands without scoring a single hit. The 3rd wave overwhelmed the ship AA and the CAP were not in their proper positions to intercept, thats why they were able to break through and set 3 carriers ablaze. The remaining carrier launched an attack on Yorktown whilst a last US attack set the last carrier ablaze, due to lack of CAP since the zeros were unable to land to refuel and rearm.