Compared to downtown Hong Kong, Japan is mostly uninhabited country. Everything is relative.
What this means is that coastal areas where tsunamis are likely are off limits to certain types of development. Farm land would be a great application for this area, for example, but not so good for high rises, nuclear plants, and hospitals. The actual impact force of the tsunami is far, far smaller than the flood area (which can be relatively easily dealt with). You're talking about the major restrictions covering a fraction of 1% of the land area.