Not an expert, but I would guess it's a combination of: 1. Shinkansen trains are run on an extremely tight timetable (often 5 minutes or less between trains).

Not an expert, but I would guess it's a combination of: 1. Shinkansen trains are run on an extremely tight timetable (often 5 minutes or less between trains). It takes twice as long to load or unload a double-decker car, so this presents a significant risk for schedulers. 2. One of the key benefits of double-decker cars is that they save space by cramming two cars worth of passengers into a one-car footprint. This allows significant passenger service in and out of small stations with short platforms. But Shinkansen platforms are not hurting for space (nearly all of their usage is single-decker trains, sometimes quite long ones), so this benefit isn't worth much in practice.