At the moment there are still breeding options, so I don't feel we're at some emergency state where it needs to be done for the Shikoku, but we're fast getting there. The Kishu and Hokkaido are in a much worse place, with health issues that can probably only be fixed by outcrossing.
However, I don't know that interbreeding the Nihon Ken is the way to fix things. If you add the Kishu to the Shikoku, you're accepting the allergy/skin/thyroid issues. If you add Hokkaido, you're adding PRA and CEA. These are very high percentage issues in both those breeds, so you're basically asking for them if you use Kishu/Hokkaido. With Akita, you're getting a whole different list of issues. Maybe less so with Kai.
Of course the Nihon Ken was originally one land race, just differing by geologic areas. So adding them back to each other little by little (genetic drift) is something that would have been happening naturally.
Adding non Japanese breeds is something that will never happen in Japan. If this happens, they will lose their classification as 'natural monument' (ten-nen kinenbutsu). The whole point of the classification of the Japanese breeds, and the founding of NIPPO, was to save the aboriginal dog from interbreeding with dogs from outside Japan. Many parts of the standard, faults (like tongue spots etc) were included because they were seen as being a sign of interbreeding with non-Japanese dogs.
Like all 'purebred' dogs, the Nihon Ken are heading to a genetic brick wall. A closed stud book does not work for any breed. You may be heading to that wall slower with some breeds, and faster with others, but the accident is imminent.
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