In the U.S. it would be possible, but unusual to say the windows of a house were up. Because of the way house windows are commonly designed, it would mean that the windows were open. It would be much more natural and more common to say "the windows were open." For a car windows, which work differently, "the car's windows were up" means that they were closed. My wife might say "It's starting to rain, could you run outside and check the car windows and put them up if we left them down?"