Recently I read an article about not using folders at all to group stuff, but just searching using spotlight/Alfred/LaunchBar from Matt Gemmell:
These days, I expect the machine to accept my query and throw the relevant set of my stuff back at me. Browsing through directory windows seems anachronistic now, and - interestingly - it also feels artificial.
Matt is a writer and he mostly lives in a fully features word processor and reseach tool so if that's the only thing you do, you might get away with it. You might also enjoy the focus that having such a constrained system gives you. If you need to develop it's a bit more complicated.
Using just spotlight works sure until it doesn't anymore (which happens all the time - to me as well) and you're left in the dark. A lot of times even if you have indexing enabled the search won't find your specific file so you're forced to search for the enclosing folder and go in manually. When it happens you will thank yourself tenfold for having a good folder structure.
Spotlight, likewise Alfred and LaunchBar, works 50% of the times, even when I search for the same files over and over, it still can't find them. Maybe I'm doing something wrong though, but I'm just using it normally. Most of the times are faster to open the terminal and use autojump to find the file that I want (if I've already browsed to it at least once).
Having a good folder structure will also make everything look and feel more organized. If you need to find something you will know how to get there even though you will be using Spotlight most of the times if you know what to look for. Whenever you don't you will need to navigate to the folder obviously.
I don't really see a decent alternative to having folders, even tags that got added in latest Mac OSX don't cut it. They're just a few and because of that their use is very limited.
The iOS solution of 'not having a file system' failed and Apple finally went back to providing a way to see files with iOS 11.
Filesystems are not going away, you can abstract on top of them sometimes, but in the end, you will end up using them, no matter how hard you try not to.