How long does it take for super-strong monsters to respawn

I don't irrigate them at all, the people in the village water them, if it is marked as field. Irrigitation would probably remove the need to water them.

No, you can't revisit these places anymore. And don't worry, you shouldn't have missed anything from there because everything is dependent on the story-line so you didn't miss unless you threw away anything there.

I will spoiler down here what happens in both islands and how to get more of the items you played with:

In

Skelkatraz: the only unlockable is learning the recipe of Monster Munchies and how taming monsters works. There is a hidden pot lid to wear to get a bit more of defense before getting your gear back but that's all.

And in

Malhala: You will unlock everything by playing trough it, and the 3 star sword, armor and shield will all drop in story line events. There is only one secret: once you find the ship of the starting game area, you can get an unique weapon from the pot where Lulu was held captive. The materials and stuff you build there will be possible to get more of it from 2 new Explorer Shores once you get back to Isle of Awakening that costs 3k gratitude points each.