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.
But this will change soon since JR East is adapting the line to go faster.
There's also a couple more reasons, namely that a double deck train takes longer to board/deboard, and that they're not very accessibility friendly. Plus Shinkansen have drink and food carts and those don't go up or down stairs.
Now some third party is allowed to provide a mediocre rail catering service, which amounts to students doing a side-job wearing backpacks with hot water and cups and a tray filled with instant coffee and tea and a few cans and packets of crisps and cookies strapped to their bodies making the rounds at seemingly random times and places on the journey. Not quite the same…
Add to that the lack of the frankly brilliant concept of can-coffee (缶コーヒー) from vending machines on the platforms and eki-ben (駅弁) and I suddenly really miss the Japanese train experience.
It's why even basic iterations of technologies requiring modification are often market failures, like the A380 requiring special gates to handle it. Boutique technologies like monorail or maglev fail even harder. For most cases it is profitable to use the less optimal but more flexible solution.
With a pretty major possible exception on the Windsor-Quebec City corridor. Large fraction of Canada's population in a span of ~1200km. Particularly the Toronto-Ottawa-Montreal span with (metro area) population totally ~11 million over 600km, a Shinkansen-speed rail would be very competitive against air travel.
They're working on high frequency rail (which will also increase speeds to ~160km/hr), which should be closer to competitive, but still not great.
As an example, the model identifiers in use by the Paris Metro have the year of the _order_ in them and we still have MP59 trains running on line 11. They have been modernised and refurbished a few times, of course, but that's 63 years of service. Talk about a ROI.
Commuter trains in urban areas tend to be used upwards of 40 years with one or two rehabilitation cycles. That said, the busiest lines generally get new shiny trains every 15-20 years with older ones being sent to less busy lines.
The recent trend (since the 90s) have been to build cheaper, lighter and less long lasting trains, so that trains around that 20-25 year mark can be replaced with ones using the latest technology. That said, I've seen those trains being fitted with the latest traction units (not cheap!) around the 15 year mark, so we'll see how long they intend to use them.
But that might apply to metro and regional rail more than long distance, so it might not be relevant here.
Shinkansen at peak time runs more frequently than even some subways line in Japan. The Tokyo-Omiya section (shared between Tohoku/Joetsu/Hokuriki Shinkansen, which E4 also ran on) runs at peak of 15 trains per hour per direction, or 4 minute heading. (The Tokaido Shinkansen is even more impressive at peak of 16 trains per hour per direction.) The loading time is very, very relevant, and it's why E4 has been phrasing out for a long time already.
My guess is that outside of the peak, these kind of trains are not necessary. And the peak can apparently be accommodated without them. So there may be some times where they would be economically advantageous, but not always - meaning it could make sense to have some double deckers.
But for train services, it makes sense to have uniform fleets, both to reduce maintenance costs and increase dispatching flexibility. Trains should also have the same performance profiles and dwell times (as mentioned before). So any small peak time advantage is undone by the bad economics of having a non uniform fleet.
But I agree, that world is not ours.
Btw, more station tracks than line tracks can also happen on regional rail, for example check out the downton section of RER C in Paris (the yellow line) [2].
[1] https://www.haisenryakuzu.net/documents/jr/shinkansen/tohoku...
For sure more platforms than lines in is a good idea that exists today.
Previously Tokaido Shinkansen only can only runs 14 train per hour (note that unlike Tohoku/Joetsu, Tokaido Shinkansen runs 14 tph over 350km of tracks, and not all trains has same stops), but after some optimization, including a procedure to reduce dwell time by a few seconds, they were able to push that to 16 tph.