I doubt it. There has been no evidence that Kobo have used different hardware for Japan than elsewhere. There are other people here with Japanese purchased devices that are installing firmware from the download links. But...
Kobo have done a good job at the hardware level. For most of the ereaders, there is an internal micro SD that has the software on it. This has three partitions. The first partition is the current version and the third where all the books are stored. The second partition contains the factory firmware. When you do a factory reset, the other partitions are wiped and this is installed to the first partition. It isn't completely foolproof, but it is very safe.
Added to that, if you want to, you can open the ereader and take a copy of the internal micro SD card. While you are at it, you can replace the card with a larger one to hold more books.
The reason your Mini is not updating, is that Kobo have frozen the firmware at 2.6.2. If you have 2.6.0, then it means a version was released for Japan, and the changes in 2.6.1 and 2.6.2 were not things that helped a Japanese user. From memory, the main change from 2.6.1 to 2.6.2 where to fix a problem in the demo mode. And I think Kobo fixed the Dutch hyphenation dictionary. Kobo release the updates based on their affiliates. It's sounds like they didn't release it to the Japanese affiliate.
Mentioning the affiliates has given me an idea. The affiliate is stored in a file. This is in the ".kobo" directory and is called "affiliate.conf". On the Glo I am setting up for my mother-in-law, this has the following:
Code:
[General]
affiliate=Kobo
People have found that changing the affiliate will change when they get the updates. If yours has something other than "Kobo", change it to "Kobo" and see what happens.
But, I think you are very safe to manually upgrade the firmware. A lot of people here with Minis ran 2.8.1 with no problems. 2.10.0 was also safe. 3.0.0 is where problems started. But, this was an issue with how the size of covers on the home screen. From the screenshots I saw, it might have been better than the proper display. I think you are safe with either 3.0.1 (the latest for the Touch, same resolution as the Mini) or 3.1.1 (for the front lit devices).