Why weren’t the Gato/Balao/Tench boats designed for the number of men assigned?

Actually, they probably had been. These submarines were originally expected have 70 men on board to operate the equipment available when they were designed. However, new equipment – often electronics - was added even before the war. Then we realized that we would require more than 70 men in a crew. Soon after the war started, a crew of 80 men became the standard.

Although the number of men in the crew had increased, the basic design of the boats didn’t change. At that point, there was simply no place to put additional bunks. It was the equipment added later, and the men needed to operate it, that caused the shortage of bunks.