I actually rely on this duplication to help me create linkages between pages in different contexts; following your example, I might have three different pages with an alias of “database” (or notes with the same name in different folders I guess, although I don’t do that in my workflow) and depending on context on my note text I want to link to different external notes.
Saying that, I do strike a similar issue to what you’re talking about - I have notes that are reviewed and “finalised”, and I don’t want to link any of the remaining keywords or see them as “unlinked mentions” because I’ve already made the decision that I don’t want to link them. It would be good to choose an unlinked mention and mark it as “ignore” (Which is a manual per-mention version of your default per-note suggestion I guess)