I feel like I should probably post, as a Japanese homeowner (as in, owner of a Japanese home), but not quite sure what point I can make.
There are tax breaks for your home loan - I believe for the first ten years, you can deduct about 1% of the full outstanding balance of your home loan from your tax liability amount. This can be pretty significant. I believe there are additional deductions if you are buying a home that is built to certain long-lasting construction standards (and is certified as such) but I don't know the details on them. Most houses are not, I believe. (At least in the Tokyo area. I imagine other areas might have other construction methods being more common.)
I'm looking at
this link, which points out that this deduction is for new homes, and secondhand homes built in the last 20-25 years or which comply with earthquake resistant standards and have a warranty. Older properties probably would not qualify, so this suggests there would be a significant tax advantage in buying a newer property over an older one.
I want to listen to that Freakonomics podcast, but it is true that the prevailing mindset seems to be that the value of your building depreciates to zero over a period of 15-30 years, and the remaining value is based on the land itself. Hopefully the value of owning land in the Tokyo area will generally increase over time, but for someone who bought during the late-eighties bubble, that may not be true. (Or it may have only recently recovered.)
One can argue that this is ridiculous, but if everyone in your country believes that your 20-year old home is worth basically nothing, you won't be able to sell it for much, regardless of how much you disagree.
Owners of high-rise apartments often technically own a small plot of the land it resides on (tens of centimeters on a side, say.) I imagine this helps put a floor on the perceived value of your unit in the building, since it is tied to the land value. I'm not sure, but I assume in other cases owners only purchase the building area and don't have the land ownership. I imagine you could get a cheaper price for those types of apartments but then they will depreciate more heavily.