I'm very happy I found this old request with some valid points. I had the same request (linked here) but did not spark much discussion.
I can give some (I think) good reasons why there is a clear benefit of seeing sub-notebooks in the notes panel: for mobile users, it makes navigation much easier. Navigating through the subfolder structure is hard when you have to reveal the tree and then un-reveal it (it requires a lot of clicks).
The worry about it taking too much space I'm not sure holds, as that is precisely how file explorers do it, and I have never felt that my subfolders take up too much visual space even if I have many, many files inside a folder. I would however like the idea that it could be a setting to toggle on and off if there is indeed someone who feels it clutters the notes list.
The analogy with email is interesting, but I think emails are very different from notes in Joplin - in that emails are "designed" to be moved between folders fluidly: from inbox, to archived, and sorted into folders, usually with very few subfolders. Notes in Joplin I see much closer to pieces of text or notes in a physical filing cabinet with folders and subfolders, which is what the operating system's file system navigation tries to mimick, and showing the subfolders inside the currently open folder alongside the notes is an important part of that analogy.