Comment by input_sh
Honest suggestion: do not worry about where to put it, worry about what you will type into the searchbar when you half-remember it 2 years later.
No file structure is ever gonna beat a good searchbar, adjust your own notes accordingly. I completely hid the file explorer. If I need to cluster things together, I use very specific key words at the top of the file (think: #Parent/Child), they're far more flexible than a file system.
I have been exploring using tags in file properties instead of a folder layout. Just so I can pull things like they are a person, they worked for this company. Or I'm only looking for project docs, or article summaries. I just haven't wholesale moved so I'm getting the disadvantages of both approaches :p
I generally think you're right though so I am moving away from folders. Especially when the notes are raw text (markdown) and can be searched by anything effectively.
I am also interested in graph searching but I haven't used it yet.