mano on the Discord channel suggested it would be better for there not to be a hover pop-up for links to non-existent notes.
As Obsidian’s fantastic dev team gave these pop-ups their own class when the note doesn’t exist, they can be hd=idden with CSS:
.mod-empty {
display: none !important;
}
(I also remove the underlining from links to non-existent notes as I don’t consider them links and I think it makes for a better user experience 
)