I’ve been doing something similar, since I have notes on a lot of topics that really aren’t related to each other at all. My notes with technical information about specific mechanical keyboard switches I own have nothing to do with my notes about trans representation in video games, and neither of those have anything to do with my notes about how to solve a Rubik’s cube, etc. etc. So when I had them all in the same folder, it felt very cluttered and confusing. And even though I mostly navigate my vault using hub notes or the quick switcher, on the rare occasion I did need to use the file explorer for some reason, it was extremely difficult to find anything. Plus I ran into the same issue you did where I kept having to include the topic in the title of notes to avoid naming conflicts, which felt unwieldy and redundant.
So instead now I have different folders like “Keyboards”, “Media Analysis”, and “Rubik’s Cube” to keep things separate, which feels a lot tidier and easier to work with. And it means I can have notes in the Rubik’s Cube folder called “beginner method” and “basic techniques” and not have to worry about them conflicting with notes about the beginner method and basic techniques for some other topic. It also means the different folders are largely self-contained, so if, say, a friend got a Rubik’s cube and wanted to see some of my notes on them, I could easily just upload that one folder somewhere, and not have to go gather all the notes and images from different parts of my vault.
A lot of the arguments I’ve seen against folders talk about them imposing artificial categories that don’t match how our brains actually work, or forcing notes to be in only one category and thus making it harder to see how they could connect to other categories. And I agree that sort of thing can happen, especially if you have a lot of notes about general concepts or ideas that are applicable to a variety of fields. And since notes can only go in one folder, you do have to be careful not to make your folders too fine-grained, or you’ll make it too difficult to decide where each new note should go.
But personally, a lot of my notes are very specific – they’re about a particular physical object, or a particular term or technique in a particular field, or a particular project I’m working on. They have an inherent context or scope, so to me representing that context by putting the note in a specific folder does feel natural, and what feels artificial is lumping everything together in one big folder and pretending it’s all related when it clearly isn’t.
(The folder note plugin works really well with this; I use it to make a “landing page” for each major folder, so I can use the file explorer to navigate to a particular context, but then use the landing page to for navigating between notes within that context, or to other contexts that one is related to.)
So far this has been working quite well for me, though I do sometimes have to rearrange folders, or let notes hang out in the root folder for a while until a new category naturally presents itself.