New houses and apartments depreciate significantly once bought, and old homes can even trend into negative territory. Land that someone has cleared for you can be more expensive than the same land with an old home on it that they presume you will later pay to demolish.
The land itself in Tokyo can appreciate, but not enough to offset the rapid depreciation of the structure. A lot of the avoidance around old homes is cultural (maybe because of frequent natural disasters), and it’s started a self-fulfilling prophecy where old homes can actually not be livable. People build homes with the depreciation in mind and don’t generally use long—lasting materials, leading to homes that aren’t actually livable a few decades later when they might be sold.
On the bright side, this leads to a lot of opportunities for architects to build new homes, so it’s also part of the reason why you see so many uniquely designed homes out of Japan.