Sorry @RatioTile, I didn't see your comment before, well that is interesting and heartening to know that the Ryuku flying fox is kept at several zoos in Japan.
Why are these subspecies being kept and presumably bred with one another ?
Also, what are the enclosures for these bats like in your opinion ?
I would hope that eventually captive colonies of the Bonin island flying fox would also be established at Japanese zoos as this is a purely Japanese endemism and one that certainly requires ex-situ.
I believe that the Amami rabbit colony that is kept at Hirakawa zoo is only down to a few individuals now and I personally think it would really benefit from being strengthened and also being kept at other zoos.
At Ueno Zoo the Orii flying fox is kept in the small mammal house, with over a dozen, with a lot of perching and things to climb around on. They climb more than they fly. Inokashira Zoo's setup is similar, but they share it with a couple of birds. Okinawa World's outdoor cage is small, but megabats kept in some rescue centers in other parts of the world are kept like that. Notably Okinawa World is not JAZA accredited. As for Okinawa Children's Zoo and Museum, they are kept in an enormous outdoor aviary about 2 stories tall, shared with Japanese wood pigeons. The Daito flying foxes are mixed in with the Orii, although from an email the staff said there are only a few Daito left and all are geriatric. When I saw them I couldn't really tell them apart, and the signage either did not mention the Daito, or did not list the species down to ssp. level.
As for the Amami rabbit at Hirakawa, where did you find this information? It's hard to find anything online about this collection, just that they have some that breed and are offshow. The only other particulary rare animal kept at this smaller zoo is the Amami thrush.