When you create a link to Note B and then copy that link into Note A, you also implicitly create a “backlink” in Note B to Note A. I don’t see that Evernote is currently able to display these backlinks (for example, with a pop-up window that shows all the notes that currently point to a given note, Note B in this case). This would be useful for re-discovering relationships between notes, and when deciding whether or not to delete a note.
It would also be nice to have a map, maybe visual, of all the links in a notebook and maybe even an entire account.