Obsidian has nested folders. Using tags to organise flatly is a choice. I organise with a hierarchy just fine - what are you looking for
Elisp authors have written package extensions (aka "plug-ins") for Org-mode that provide even more powerful and specialized note-taking. Among the most popular today are org-roam (built on the zettlekasten method) and denote.el.
Also, at least for my use case which is to find random notes I took about stuff 2 years before and that's hidden God knows wheres, I find the way Zim does it to be superior because it allows fuzzy searching on a note basis.
For example: you can't remember how to kill and recreate a new default-vm to fix docker-machine, you search "default vm", and it will find all the files that have both "default" and "vm" in them, even if they're not on the same line.
The way Zim implements that is it creates a file for your note, then creates a folder that contains all the images you put in that note and any subnote.
You could technically do the same in Obsidian, but I don't want to micromanage the file/folder structure.