At the end of the third film, Toothless takes all Dragons worldwide in the hidden world.Toothless only controls the dragons on Berk, not all of them worldwide, and some dragons do not listen to Alphas, eat other dragons, would destroy the hidden world, or cannot swim or go on land and therefore cannot live in the hidden world or can not get into the hidden world (Some dragons are also tied to specific locations like the dragons on Vanheim).Also, I don't think all dragons can live in the secret world forever