I was trying the same way but I gave up and now I have a semi-structure.
I don’t do a pure Zettelkasten, my archive is a combination of work and thesis related notes and Zettelkasten notes. The folder hierarchy also represent a graph (although a really simple one) but at least for me it helps with discoverability (when I have a note about atomic topic that I am currently learning/making research it helps to have it in a space that I could look more often)
I also recently use Ulysesses App for editing (since half of this year it has a possibility to import external folders), Obsidian is only for creating and moving, linking notes. Ulysses (and Zettlr) has one pane for folders and another for files, for me it give a cleaner look.
It also help to have notes in project-related folder, this is what Tiago Forte proposes (The structur emerges itself and I have a sight of what I done in a specific project)
