So, while I'm not trying to head cannon the population is healthy (they're very much still in danger) but, the reason night furies are so rare in the archipelago is bc they're mainland dragons. What do I mean by that?
I mean objectively night furies are significantly more bat like than is truly acknowledged.
For example, I believe night furies are NOT cave dwellers. My reasons being that
1. We see both in the first movie, and I believe at least twice throughout the TV series, that Toothless' claws aren't actually that good at gripping stone. If night furies were cave dwellers, do we really think toothless would've been stuck in the cove cuz he couldn't CLIMB SOME ROCKS??
2. How Toothless slept upside down with the tree and how he snuck up behind Hiccup the first time (that's less bat related but is related to being not cave dwellers, I elaborate below)
And so my head canon; night furies live almost near-coastal but slightly more inland, in large, hollow trees (I'm talking like ancient forest level growth) hunting by prowling along like a panther (hence as he snuck up on hiccup) and flying between branches, living in small but likely multigenerational familial groups most of the time, but there's definitely some kind of migration as well, hence why they're good long distance fliers, during so they fly over the archipelago and maybe that's how toothless got lost or stuck away from his group