I believe that they were arming their planes for a second strike on Midway, when an American carrier was sighted.
They then started switching to ordnance for attacking ships, and left the general-purpose land bombs on the decks until they could be stowed later.
Whoops.
They were also resting their air crews. After a couple of strikes at Midway they were gassed. The air wings of Hiryu and Soryu were pretty small compared to their bigger sisters, and also when compared to US carriers. Essentially they had no reserve aircraft.