The total for the whole attack was 29 shot down and about 121 damaged. Of the damaged total, many were only superficially damaged. Assuming 70 of the total had too much damage to be certified for flight again that day and 50 could fly, Nagumo "only" will have had 300 aircraft, or still 80 more than at Midway. Assuming NONE were able to fly again that day, Nagumo will still have had 250 aircraft immediately available, still about 20 more than at Midway.
So any way you slice it, there is no explanation for no follow up attack.
How long would it take to prepare, lauch, execute and recover another strike? Given how tight the fuel situation was, could he afford to stooge around for that long?
Further, even if there were absolutely no U.S. submarines about, Nagumo couldn't know that. Every hour he spent in the area meant (as far as he knew) greatly heightened chance of sub attack. Or carrier attack. Or land-based air attack. As far from home as he was, a damaged carrier likely meant a lost carrier. And Japan could not afford to lose even one.
Arguments that it was a mistake not to launch a further strike seem to hinge on Nagumo have perfect intel, as if in a wargame.