Of course there are lots of old temples and shrines but even those have often had every single piece replaced. I was really surprised a couple of years ago when one of the local shrines tore down their building completely and rebuilt it exactly the same!
Whether this has to do with earthquakes or not, I'm not entirely sure. My wife and I have been thinking of buying a house and I keep having to remind myself that I will lose money if I ultimately sell. Our current plan is to wait until we're a bit older and then buy a not-too-old used house at a discount ;-)
It was known that older houses were dangerous in earthquakes (I believe the safer building code dates from the 80s), but no one was really worried about it until the Kobe earthquake where most damage was borne by older buildings.
But I do understand and partially agree with your primary point.