My purposes might be different than yours, but for me it’s very clear.
I do research in the humanities that requires interdisciplinary methods.
So tags are concepts or ideas that are typically referenced (implicitly or explicitly) by a wide range of scholars across varying disciplines.
Links, on the other hand, are for the argument of a particular theorist/scholar.
Notes/pages/links are typically an article, chapter, or book of a particular theorist/scholar. Or it can be an edited volume where each chapter will have its own link (almost like a TOC); conversely in the corresponding note of that chapter/link, I have a link back to the edited volume/TOC.
Maybe another way of putting it is: tags = concepts; notes/links = arguments of a particular author (which is usually a journal article, chapter, or book).