The Azuridae and Crawlers in those caves do indeed respawn, and have for pretty much ever. It's *probably* not a factor of you completing the quest, and rather a factor of you taking long enough for the respawn timer to tick over.
It's about as out-of-the-way as a place can get, and it's a great place to farm up better quality psi beetle shells and crawler poison for endgame. Hopefully it is, as it appears, intended. If it's too much of a hassle, there's a southerly path out of Dude's caves that will bypass the Crawler map, though you'll have more Azuridae instead. Six of one.
