I have tons of folders because I started using Hazel within months of getting my first Mac, and I've grown to use it more and more as I've grown to learn my Mac.
Several are under a common folder ("Launch" -- my base folder for most scripting and automation), but many are not. Some of them have similar rules, but many do not. Many have only 1 or 2 rules per folder, but a few have 10 or 15.
Launch: 18 rules. Most of these launch apps based on the names of empty text files that I upload from my phone (which I wrote about years ago
here). Others automatically start torrent files (also so I can upload them while on the go), and one I think is particularly clever
gives me a push notification when Comcast fixes my internet (since it goes out often enough).
One folder monitors OmniFocus and automates logging my completed tasks. Several others monitor my various plaintext apps' folders and automate processing / moving / renaming / archiving text files. A few others automatically prefix filenames with the date they were added to a folder for easy sorting. Others process screenshots or monitor my ~/Downloads folder to open files in their respective apps.
Another monitors a folder I used with an OpenMeta tagging app and automates pulling those files and their tags into Evernote (
using a script I think I found here). Some process files that are downloaded from emails to Dropbox by IFTTT, or run scripts to automatically post content to various sites using Python
and/or AppleScript. I have a script that runs
whenever I connect my Kindle and processes my Kindle Highlights into a format I like in order to more easily post them as "favorite quotes" to my site.
If you can't tell, I really use Hazel for quite a bit, and I think it's an awesome tool. I'm not sure if I'm just a big outlier, but I wouldn't be surprised if there are others using Hazel to monitor more than just 4 or 5 folders, and who would benefit from some kind of sort or search feature.