I propose that visits to the Moga Ruins or similar waters by Ceadei are perhaps extremely rare occasions, and the reason they are seen rarely is that they spend the majority of their lifetimes in much deeper waters. This would explain both that they were considered "Mythical" and that the even rarer Goldbeard  Ceadeus seemingly allows itself to go blind. Following this logic, the Common Ceadeus would visit these shallower waters more often,  and therefore take care to file it's horn down so it could see.

Considering the extremely long lifespan of the beast, it could spend several years in one general area before deciding to leave to another, and could stay in a place of its liking indefinitely.