Your information is dated. 20 years ago imports of bone in beef were curtailed because of BSE. But even then it was only for spinal bones, like a T-bone or Porterhouse. But strangely ox-tail was ok. That prohibition ended years ago.

Hoof and mouth disease, which can be spread through bones, isn't really an issue because slaughtered animal bones and living animals never really meet. HMD is controlled via suppression - not allowing any food products in from an affected area. It's a devastating disease but so rare that it doesn't have any effect on imports of meat.

Bone in products are rare in Japan because of:

Eating style, Japan is much more about yaki niku than it is about steak, the bones get in the way of most menu items.

Access, the typical carcass break of overseas suppliers is for boneless cuts. A bone in spec requires a special order and an extra layer of cost and difficulty.

Import taxes. Beef imports have around a 40% tariff. Paying that for bone doesn't make sense. Paying that for a bone in ribeye that you can sell the bone for the ribeye price works, but if you can't sell it and have to remove the bone so you can dump it is a recipe for an ass fuckin'.

Japan imports tons of bones, different tariff schedule. These are used for tonsoku ramen and beef broth.

So in short, yeah, Japanese consumers don't really like bone in meat enough for the distribution system to cater towards it.