As someone coming from Ulysses, which has a really powerful smart-folder system, I really miss this feature. Here’s why:
I’m a grad student so I like to use tags that reference topics, as well as tags that reference authors when I’m taking notes on a book, and ‘place’ tags that reference where the note came from (lecture, book, paper, conference). Given that these tags are of different kinds, I want to separate my ‘topic’ tags from my ‘people’ and ‘place’ tags.
My workaround is to use nested tags, but this isn’t perfect because I really like adding my tags inline as I write on the fly, and it’s really clunky to do this when you have 3 nested tags (and it doesn’t read nicely either).
The problem with using Hazel as @vishae suggested is that it still uses a traditional folder system whereby one note can only be in one place. The idea with the smart folders is that a file can be in multiple places at once. A file on a book on Einstein, for example, can be both in the ‘people’ folder under its author, and in the ‘topic’ folder under ‘physics’, ‘time’, and so on.