I use notebooks and nested notebooks heavily. I've found that a directory-style structure works well for me, especially because the integrated search is also good if I forget where I put something. I have never personally had success with tagging for organization, but maybe that's just me.

In no particular order, I recommend:

* WebDAV to sync your files, I just use some of my fastmail storage and draft off the $5 a month I already pay them

* Pasting screenshots from your clipboard into your markdown works automagically on desktop, drops the file with a generated name into the Joplin file structure. It elevates the tool quite a bit imo

* It is worth getting comfortable with some of the basic markdown annotations. Just knowing to use asterisks and underscores and whatever speeds you up a lot from having to go click the "bold" button or whatever.

* I really like editing with the preview pane open. It closes the loop for me, and is the best of both worlds where I get to just type the annotations at my normal typing speed, but also see the formatted output so I can make changes as I go.

As a Logseq user I'd say that your last sentence/question is correct. The graph that emerges from your page references forms the primary form of structure. If you want to be able to find X by searching for Y, either mention Y in X or tag X with Y. In addition, though, when you have a page foo/bar/baz, foo and foo/bar also become their own pages (not folders per se, although they'll show baz as a child) which does let you get a folder hierarchy if you need it (and every folder comes with an index.md, because it's a bona fide page). Especially useful for nested tags like #movie/comedy.