Honestly, the food issue strikes me as something that would take the wheels off of the Japanese defense in late 1945. Could they even get sufficient amounts of food and ammunition to the front lines mid-battle while getting bombed?
Food and ammo would become an issue, but not until the defenders had mainly been wiped out in any case. Units were being deployed with two units of fire, although some were coming up short there is a reasonable chance that this would have been made up by the time Olympic actually took place (after the delay caused by the October 1945 typhoon). Once those troops had expended all their ammo, it really wouldn't matter since there was no real plan to withdraw. Troops would stand and die, in place, along with most of the militia and a good percentage of the civilians in the combat area.The IJA and IJN planning expected their forces to be wiped out, just as they had been across the Pacific. The Japanese had 450,000 combat troops on Kyushu, not counting the "volunteer militia" (in August of 1945 the Japanese had 2,350,000 troops under arms IN the Home Islands, plus several million other quasi-military employees of the Army and Navy, plus a "volunteer" force that numbered over 25 million, although it is doubtful more than 15% of this last group would have actually appeared). The Japanese did not expect ANY of those 450,000 troops to survive unless the Allied invasion was driven into the sea.
The Japanese had a very well designed defensive plan, with some "innovations" that would have caused massive losses. In another thread on the subject of the invasion I discussed the underwater swimmer plans, including the underwater "bunkers" for sheltering the swimmers until the time to deploy, something that the U.S. never even suspected to exist until after the surrender. The U.S. would, best case, have suffered more losses than on D-Day BEFORE the first U.S. boot touched the beach. The Japanese were well aware of the power the USN could deploy via the gun line and what American air power was capable of, their defense plan called for troops to be IN PLACE prior to the invasion (the Japanese had correctly identified ALL the landing beaches, not just on Kyushu, but on Honshu as well), with any movement being by small units to prepared positions, often using natural or man-made caves/tunnels.
If the Japanese didn't suffer at least 500,000 KIA (including militia and "collateral") just in the taking of the southern third of Kyushu it would have been a miracle.