Village Sim, like Plant Tycoon and Fish Tycoon, is only saved when you exit (either to another app or the launcher), so I usually exit once in awhile just to make sure I don't lose the progress that my villagers have made.

Your villagers shouldn't have just disappeared overnight, though, and on normal speed the skeletons shouldn't have had time to decompose (if they had died). I'm afraid I can't explain what happened to your villagers, unless they just starved or died from sickness. The villagers are not as productive when the game is off, so that's possible.