Unfortunately I don't have a comprehensive answer but since there hasn't been any other activity here I'm going to give some hints based on what I remember.
If I remember correctly, the core notification system works by combining a notification type with a subject ID, then some notifications are suppressed when the type+ID already exists and is unread.
So for example if you get multiple likes on the same post, they will be merged together as one in the notifications dropdown. The mail version of this notification would take a look at whether the merged notification has been marked as read, and if not, no additional email will be sent.
I think that's where mentions become tricky, and also compounded by the fact mentions and quoted replies are the same thing internally. I think the mention is also suppressed by type "mention" and the mentioned post ID, so you'll only get one notification for a given mentioned post, even if multiple other posts, even across multiple discussions mention it.
I am not entirely certain of all of this, and it's possible some things have already changed for the upcoming 2.0.
Those were part of the difficulties I had when working on the Blomstra Digest extension, as that extension essentially un-merges the notifications and bundle them back together a different way from what Flarum does internally.
