It was Shokaku that had a bad flight deck: three 1000 pounders from SBDs will do that...and Zuikaku was hosting what remained from both air groups. Shokaku wasn't out of the yard until June, and wasn't combat-ready with a new group until Mid-July 42.
One thing to keep in mind is that the Japanese were having production problems delivering new Kates and Vals to the fleet. Nakajima was tooling up to get the B6N Jill into production, and had to restart the Kate line to fill attrition. Similarly, Aichi was about to start building the D4Y Judy (though it had been designed by the Yokosuka Naval Air Arsenal), and had to restart Val production. Only Mitsubushi was free of the problem: Zeroes were coming off the assembly lines in needed quantity.
If Midway is delayed until July, then the TBDs will have been replaced and at least the VT squadrons will have gotten enough stick time to be proficient in the aircraft, and log some traps in the meantime. It also enables Pacific Fleet to have three two-carrier task forces.