>>49726938 (OP)Because a lot of the older buildings either got burned down over time for various reasons, destroyed in earthquakes, or got bombed out during the air raids of WWII. In the past, they would simply rebuild these things in the style of architecture they were most familiar with, but in the Meiji era and onward, they began taking more inspiration from west for not only reconstruction but also new builds. In a way you can blame modernism and more experimental styles of architecture taking off in the west for the aesthetic state of Japan's modern architecture.
You might be surprised by how many of the great temples, shrines, and castles you currently see in Japan are not the originals. Turns out making everything out of wood is not good for longevity, especially in a country that has been as historically wartorn as Japan.