In the final episode, Hikari's father explains:
Children born to a person of the surface and a person of the sea lose their Ena. For this reason, the people of the sea had to hibernate before the surface met its demise. We had to make sure that there were enough descendants to leave behind and that there was a chance at a future.
Hibernation in this series seems to be equivalent of Cryonics. Which is where an organism is preserved for virtually an indefinite amount of time by being frozen. During this process, the organism is frozen in time and does not age.
So the belief is:
- There's an apocalypse coming. And everyone on the surface will die.
- If the entire population of Shioshishio marries into the "surface people", there will be no one with Ena to survive the apocalypse.
- So the only way is to hibernate through the apocalypse.
But then Hikari's father continues on:
But Miuna prove me wrong. Miuna has Ena now. That means there's hope for the future even if we wake up.
This is why everyone wakes up.
So biologically, there is no need for an individual to actually hibernate. That's why Chisaki is fine having been on the surface the whole time.
On the other hand, there's nothing in the Anime that seems to explain why Hikari, Manaka, and Kaname woke up naked on the surface.