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.