No, you're right. Northern Japan isn't as densely populated as the rest of Japan, particularly a place like Tokyo, but you have to remember that Japan has nearly the same population as the US in an area the size of Montana, much of it along the coastlines. If it hits 20 or 30 towns up there with an average of several thousand dead per town, it could really get ugly fast. There are also currently a lot of people that are probably trapped, or injured, or cold, and there are a lot of fires burning.
Sumatra didn't feel like there was going to be that many casualties and it went from 75,000 to 200,000 alarmingly fast.