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.