I do add Habitats almost every time (and upgrade them) and I continually check the status of the penalty number to see if there is any change in the housing penalty. But I have never seen it go up by more than 1 in a positive direction. =( I've tried adding more tunnels as well but without any improvement still. It actually seems to go in a negative direction slightly a lot of times even though I've gotten my habitats and apartments to have less people in them. And I have tried taking down the apartments after the habitats are up as well. Guess I'll try adding skyscrapers more often where I can to see if that helps as well.
Dune was the first thing I thought of when I first saw the worms as well. Would be pretty cool to see them go that direction with the game. I never got really got into the movie or books but have heard good things.