I always though it was a ancient Sheikah Tomb that was taken over by Necromancer type people who worship a dark God. And the Dead Hand was one of the Necromantic experiments turned loose. Maybe the guy who lived in the house where the well is was secretly a Necromancer. And the well was his secret lab or something. And Perhaps Bongo-Bongo was the dark god they worshipped. If it was a tomb, though why would the dead bodies be lying around and not in a casket or something? Hence, profane experimentation.
But my theory is a little out there.
