What you're stating is a gross generalization and untrue in a literal sense (probably easy to realize if you remember how things were a decade ago).
While Y!J and Y!Inc are separate entities, the former does borrow/use technology from the former and some of the Y!J services use Y!Inc servers and/or services maintained by Y!Inc.
Y!J user ids are completely separate from Y!Inc though (Y!Inc ids are shared through out the Y! locales).
It's been almost a decade since I was at Y!J, but from what I understand Y!J does continue to leverage the Y!Inc relationship for services and servers.
Additionally, simply stating that old technology is the reason for a security breach could be a red herring, it isn't always the age of the technology but how it is implemented.
I would characterize the comment as more like "Attitudes towards development practices are a decade behind" (rather that the tech itself necessarily) which sounds pretty accurate[1] for most Japanese companies that are not part of the newer "Gree" wave.
There are definitely a lot of opportunities for innovation in Japan. This excellent post by a co-founder of MakeLeaps, an invoicing startup founded by gaijin, covers some of the difficulties (and opportunities): http://www.makeleaps.jp/blog/en/2012/05/everything-ive-learn...
And to put this in context, IT in Japan is about a decade behind the West.