You are running up against a fundamental design choice of Obsidian and a fundamental limitation of storing documents as plain text. By using portable flat files in folders, it gets to be a big pain in the butt to deal with multifile documents. That’s just what it is, and as far as I know, nobody’s done a particularly good job dealing with it.
One of the core observations underlying Obsidian and other linked-note systems is that all deeply-nested hierarchical systems for organizing your notes suck, and perhaps are a trap. So your concern for the cleanliness of folders is a pain we all have felt, and still feel! but also is paddling upstream with what Obsidian wants you to do, as you’ve observed.
I don’t know your use case. But in my use case, I’ve reached a few (like 3) high-level folders that I sort my notes into, and there is no hierarchical organization below that. This is part of the approach that a lot of folks have arrived at as well, through help from the zettelkasten.de folks and Nick Milo and the like. EDIT: to be clear, there are hierarchies among notes, but they are defined by the notes themselves in their content. This approach is much more flexible than folder management, recognizing the difficulty of categorizing ideas.
So think through what it is you’re trying to do. Why is proper sorting by folder important to your use case? Can you solve the problem differently? Do you have a subproblem that’s better-suited to a different tool?