Not to sound like a 50's handyman. (http://www.familyhandyman.com/doors/repair/fix-sagging-or-st...) However, replacing / rehanging doors and windows and doors is generally a fast and easy thing to do and more or less required as wood flows and settles in an older home. Really what your talking about has more to do with a generally mild climate enabling a lack of maintenance vs. any kind of earthquake damage.

PS: I stayed at a a 100 year old farm house made by complete Amateurs and built on over time where some of the floors and trim sloped more than 5 degrees which is vary noticeable to the naked eye. Yet it had decent insulation, every door opened freely and most windows opened just fine. It took a few people a few weekends to get it there, but vary little cash. A respectable carpenter can do the same thing for you for about 10k every 15-20 years. Again though the difference without cold winters there is far less incentive to actually deal with such things.

Edit: The science behind it is even fairly interesting, but basically wood reacts to the forces on it over time so the less symmetric the home the more extreme the warping can get. Which again hurts Japan with there love of unusual shaped wooden homes.