1.) Cost (mostly in the labor rather than materials, and because of less standardization probably)
2.) [1]Earthquakes. Unless you do extra steps (which add more cost), it's much likelier to collapse in an earthquake.
3.) Harder to tear down for new construction. (More of a city-planners nicety than a homeowner's consideration, but still there.)
Probably a couple other points I'm missing.
But reinforced concrete structures are a different story. Concrete and masonry itself is brittle, but the steel rebar reinforcement adds flexibility and and tensile strength to the concrete. With an adequate design it is as safe or even safer than lighter wood structures, considering that it's inherently more fire safe, which is a big safety concern post quake.
Taiwan homes nowadays are mostly built with reinforced concrete structures and those modern buildings behaved very well in the 7.4 quake earlier this year.
This is somewhat outdated. People buy used properties all the time; it's not the 80s any more, and people don't have money to waste tearing down houses after 10 years, and people move around from time to time because of work etc. It is true that used houses depreciate, though, over a 40+ year time span, but the land in desirable areas (e.g. Tokyo) generally appreciates.
>it seems like they aren't built with permanence in mind.
That's exactly the same as in America, worse actually. Have you been in an American house built in the last 50 years? They're poorly made, by unskilled labor after being designed by people with no formal education. Japanese houses by contrast are designed by architects and engineers and made to withstand extremely strong earthquakes (required by strict building codes). They generally aren't made to look luxurious, however, so you won't find granite countertops and other stuff like that that American houses tend to add to try to look like mansions (i.e. McMansions), and tend to use a lot of pre-fab materials that are quick to assemble.
>Japanese houses I've been in have been ice boxes with little insulation and a large dependence on portable heaters.
It sounds like you only visited houses built in the last millennium. Mold is a big, big problem in many parts of the country so ventilation tends to be prioritized over insulation, and energy efficiency hasn't been much of a concern until more recent years.