… if you want to use a system as an aid to writing and as a thinking tool you should opt for a system that is powerful enough for a lifetime of thoughts. So, watch out for folders and projects. They are the means for dealing with encapsulating and limiting complexity. In addition, they hinder the most productive way of knowledge production: the interdisciplinary part.
… I think that this is one of the reasons why many retreat to project-centered solutions, curating one set of notes for each book, for example. The problems that come with big and organic (= dynamic and living) systems is avoided. But so is the opportunity to create something that is greater than you.
I liked the suggestion of hashtags and double-hashtags to indicate layers of structure in an interdisciplinary note archive. I suppose, in some systems or software, two layers of structure could be indicated without hashtags but with tags (structure) and categories (super-structure).