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.
But this will change soon since JR East is adapting the line to go faster.