>>1818659>>1818856>>1818985Tokyo-Hiroshima is broadly comparable to the Washington-Boston Northeast Corridor distance-wise. The Northeast Corridor only has 11 at-grade crossings, because its frequency, speed, and density of built-up areas made elimination viable.
Major cities also tend to lack at-grade crossings for intercity rail.
Outside of that, when you've got thousands upon thousands of km of track through mostly flat, mostly unpopulated areas, there aren't real cost/safety savings to viaducts/berms.