Why do I leave them down while stored? A few reasons;
Ours is stored inside a nice warm garage. If I want to do any work in the MH over the winter I don't want it rocking about. I have a real issue with motion sickness, I like the jacks down.
Secondly, why not? Much like the MH doesn't care neither do the jacks. With the jacks down they're there to help spread the weigh load around a little. Not a big deal by any stretch but spreading the load around can't hurt - might help.
Back when we stored them outside I don't think I ever put the jacks down, so it's not a big deal either way I guess.