I seem to remember NPCs in Oblivion stating how Juib "Drove them out of Morrowind" rather than kill them all, and I don't remember reading in his opus or through talking to him in Dawnguard anything about extinction.
Theres nothing to say they are gone forever, but I doubt they will return in Dragonborn.
Also I sincerely hope they will not return.
http://www.uesp.net/wiki/Morrowind:Cliff_Racer#Cliff_Racer
"Cliff Racers are large flying creatures found throughout Vvardenfell. They are very aggressive and will attack anyone in sight. Cliff Racers have good vision range, and will often detect and follow the player without being noticed. This can result in swarms of them descending upon the unwary adventurer.
The development team has admitted that the sheer number of cliff racers in the game was a mistake.
(lol)In Oblivion,
Jiub is said to have driven the Cliff Racers off the island and was made a saint because of it."
So, yes, he drove them off Vvardenfell, nothing more. They aren't extinct by any means. They're all probably living in some cave in Blackmarsh.