I imagine it being implementable by simply using anchor-based links as in vanilla markdown, no? So every reference can be written manually, and in order to make it convenient you only need some button in the editor, that performs quite a simple macro: add a superscript index with a link, and insert a little piece of text in the bottom of the document (or on a separate page) + an anchor.

But, it reminds me, there also must be a way to easily link one note to the other you wrote. Which isn't always available.