There is a 25% base chance to spawn Charybdis. I confirmed that he is indeed spawning when you have all the necessary items at the correct location. I had some lucky streaks where I fished him up within 1 or 2 bait uses as well as some incredibly unlucky streaks that took as many as 13 bait uses.
So the answer to your original questions, yes he is spawning and yes it is possible to fail to fish him up.
I did note that the bait bonus from the Fisherman’s set was not being applied to the attempts to fish up Charybdis and have submitted a problem report on this issue.
Thanks for the specific information, that helps me to troubleshoot issues a great deal.