I favor the same approach. In my case, I use org-mode instead of markdown as it offers a few niceties when editing from Emacs. But irrespective of that, IMHO plain text overrules any other choice as it is future-proof and can be composed with your favorite tools. For example, a VCS like Git.
I have many files in a flat zettelkasten-like structure [1]. That means, essentially, having one file per concept and using links to chain them.
That assumes that the text in your notes uses the vocabulary you'd expect, and isn't misspelled. Neither of those are guaranteed if your notes are snippets of other documents (a common EN use-case) rather than text you wrote yourself. Especially not guaranteed if the snippets are images where their textual representation is the output of an OCR algorithm.
Is there something like ripgrep for fuzzy search?
My folder tree is fairly flat and folder/file-naming is self-explanatory, so when I have to use the dropbox client on mobile, finding stuff isn't too bad.
I abandoned EN around the time everyone else did for a Dropbox synced folder full of markdown files. I use Sublime Text as my client on the desktop.
For my particular use case (I never really used the advanced EN features) it's worked well. I never really created notes on mobile, but I can read them using the Dropbox app.