I can definitely see it when your main workflow are projects, I assume PARA systems would be something you, or you already use it.
However, I think linking could be useful for you to create dedicated notes (atomic notes) that you would use everywhere, so you don’t duplicate info. Like Customer Note for example, with all information about the customer and then links to the project for that customer.
I’m a “search guy” first 
So folder aren’t important, I search for my information, by filename or full-text search.
I create notes for my projects, draft inside this And refactor out to separate multiple atomic notes.