I think it's just an old design. At the link I posted above it explains that they flood the area between the spent fuel pool and the reactor core with water to move fuel into and out of the core. So proximity is needed during this phase.
Newer designs may have below ground level storage for spent fuel.
I've also seen speculation that the pools that are heating up may have small water leaks causing the loss of cooling water.
Newer designs still have the spent fuel pool at an elevation that allows a horizontal transfer of the fuel rods between the reactor and the fuel pool.
Earthquake zone is why the rods are above...concern that in ground could fracture the container....or something like that....There was a piece about why they opted for above ground.