I don’t know what transportation you referrring to but the USS Barb was still sinking shipping and a train in 1945.
At the link below go to the paragraph near the bottom that starts with “Her 11th war patrol began”.
The Barb was busy to the end of the war.
https://www.history.navy.mil/browse-by-topic/ships/submarines/barb-ss-220.html
Yeah, BARB sank a train, and continued to wreak havoc on the Japs until the bitter end. OTOH, the big freighters and tankers the submarine service targeted earlier had largely ceased to exist. Jap shipbuilding simply could not keep up once the torpedo problems got fixed.
Ok, there was very little transportation left by 1945. You happy now?
Point being there was no way to transport any of the rice harvest to remaining population centers.
Trains, railroad yards and bridges had been destroyed by bombing. What little fuel Japan had was mostly reserved for military use. Trucks and boats were "targets of opportunity" for American fighter planes.