What's the deal with them? If they want to be Korean, they can move to Korea. If they want to be Japanese, they can become citizens. What good is the middle ground?
Picture this, if you can. You're a typical second or third generation Zainichi Korean who has lived in Japan all your life. You went to a Japanese school and only speak Japanese, not Korean. You're proud of your Korean heritage in much the same way as are many second-generation immigrants in other countries, and may have relatives in Korea.
Can you not see how this is a difficult choice? On one hand, to go back to Korea would mean plunging yourself into an unfamiliar country speaking an unfamiliar language with no prospects. On the other hand, becoming a naturalized Japanese would mean renouncing your Korean citizenship and sacrificing part of your heritage in a way that many countries other than Japan do not demand of their naturalized citizens.
It's not as simple as you make it sound, and it's no great surprise to me that many Zainichi Koreans have opted not to make the choice you offer them.