The Japanese economy does not depend on a small handful of companies that are too big to fail. The Korean economy does.
Most of the large Japanese conglomerates do not have any kind of central control, and the top companies in the group are relative equals. They are not heavily dependent on each other. If one of the companies were to exercise poor judgment, most of the rest of the companies in the group would be fine. In contrast, Samsung may be incorporated as multiple companies, but one family and its loyalists call the shots at every company within the group. If that small group of people were to exercise poor judgment, the entire Samsung group would suffer.
It therefore is entirely possible for Samsung to fail as an entire company, just as Daewoo did in the late 1990s due to poor decisions and criminal fraud committed by the family that controlled it. Just like Samsung, Daewoo was a group of companies that transacted in many industries, but that didn't matter because one family called the shots at every company within the group. Samsung could fail in the same way.
Furthermore, about 20% of South Korea's GDP is produced by Samsung. There is no comparable situation in Japan or most other developed economies.
I do not disagree with your statements with regards to Korea (they match my relatively untutored understanding), but I would not describe my understanding of Japanese megacorps as untutored, and I find myself in violent disagreement with this line.
What's your over/under on what percentage of Toyota Industries' revenue comes from Toyota Motors? What is your over/under for what portion of the shares outstanding of Toyota Industries that Toyota Motors owns outright, in its own name?
The control issues are... nuanced. The financial entanglements? They're not nuanced.
In 2011, Foxconn's revenue was 20% of Taiwan's GDP. Nokia's revenue was also 20% of Finland's GDP.
Precisely because the domestic market in Korea is small compared to Japan's or any other developed country. When you have a worldwide market leader industry coming from a small country, this situation is bound to happen.
EDIT: note that in other developed countries you see the exact same phenomenon at region/metropolis level - look how Detroit was dependent on the whole GMC business and factories. This is the very same thing at play at a different level.
If you remove their top three automobile companies and their top 3 Shosha firms (and maybe UFJ + Mizuho), they are not in good shape.
Every European country has it's handful of companies that have consolidated and by their supply chain drive a huge part of the economy.