That was exactly Nagumo's reason why he ordered the scuttling of his stricken CV's. The option of towing back stricken hulks across the Pacific was not a very tempting option, so to get rid of the stricken hulks was the best option, primarily as the towing would be at a creepingly slow pace, taking months at least before getting back in Japan, besides acting as a magnet for enemy attacks, as Nagumo by now must have realized the USN was still capable of striking him with aircraft, while he could do nothing in return.
Secondly the inflicted damage was such a heavy one, even if returning the stricken hulks back to japan, rebuilding the CV's on the damaged ships was a seriously challanging project to say the least. (Building a new ship from scratch would have been easier.) Basically the ships were burnt up above the waterline and internally completely destroyed. This left just the bare hulls as a base, with not much else in terms of engines, boilers and other internal systems. (Except Kaga which was holed by a large internal explosion, possibly her bombstoremagazine, and going down even without scuttling. Akagi, Soryu and Hiryu were scuttled by putting a few torpedoes in them, which holed their hulls to flood them. Note in this time USN torpedoes were still horribly unreliable as the failed scuttling of USS Hornet would show a few months later.)
Something technical: The box system of hangars on their own are not the main cause of making a design more vulnerable to damage, as the system did work fine in other nation's carriers of similar layout. It was the nature of AVGAS pipelines and other fuel related systems that were the primary reason of the IJN CV's being such fire hazards. British CV's build as such all had armored box style internal layout for hangar and ship sides, which worked pretty well, especially with the armored flight deck in Illustrious class and succeeding ships. Unlike Japanese CV's the British used CO2 gas to fill their pipelines when the ship was under attack, preventing such horrors as the Japanese would suffer time and time again. USN CV's too did this in most cases, unless hit by surprise in some cases. (Like USS Wasp, USS Princeton, USS Bunker Hill and USS Franklin to name a few.) The biggest advantage of the internal armored box style hangar to the open superstructure style, mostly used on USN CV's and a few Japanese, is the strength offered by such a system when taking direct damage from weapons, where lightly build superstructure style hangar's and flightdeck are more prone to crippling damage to force the ship out of the combat, being incapable of further operations, as the hangar, or flightdeck is incapacitated an unable to be repaired at sea. (Even nature can cause this sort of damage btw.) The best examples were proven when the Kamikaze attacks were done on both USN and Royal Navy carriers, with USN Carriers being forced back home to repair their gutted flightdecks, while the tough British CV's were barely scratched.