Where they are located near populated areas, you should absolutely kill them. The Fereldan Frostback has already killed a number of people and is breeding more dragons. The Northern Hunter in Crestwood bit the head off one guard and has a voracious appetite, so it will probably kill more people. Your agents in Emprise Du Lion make it clear the three dragons in Emprise Du Lion will eventually threaten the local populace.
You should kill the Abyssal High Dragon because the Venatori want it as a prize and it will push forward the field of draconology. With the others ... I'm less clear on your motivations, aside from "They drop great loot and give you big boosts in Influence."
I guess you should keep in mind that the dragon population seems to be exploding, and since they're an apex predator, it's literally up to a handful of dragonslayers to keep the setting from devolving into a
Reign of Fire scenario.
Let's keep in mind that Professor Frederic doesn't seem to object to your dragonslaying, and his entire field of study is dragons. If he thought there was a danger of the species disappearing, he probably wouldn't point you towards more dragons.