I've always wondered about this as well. The fact that Choi's: A) actual time in Japan, B) from whom he studied what has never been authenticated never really concerned me. The Aikijujutsu influence on Hapkido is painfully obvious, so he would have had to have studied Aikijujutsu from SOMEONE at SOME POINT in his life. No such techniques had been practiced in Korea prior to that...at least as far as we know. Or at least, those techniques were not native to Korea.
This kind of thing illustrates perfectly one of the reasons why efforts to connect present-day MAs with ancestors in the dim past have to be viewed with extreme skepticism. The fact that we can't authenticate critical details about the source of even recent fighting systems—stuff that happened in the 20th century, in fully literate societies—stuff like the line of transmission of Hapkido, or exactly what the training practices of the Tang/Kong Soo Do kwans of the early 1950s actually consisted of—is a powerful warning about the reliability of folktales of the past which purport to derive the martial arts of Asia from the supposed visit of Bhodhidharma to the Shaolin temple sometime way back when, or the claim that this or that modern system established in the past fifty years or so can be traced to combat systems hundreds or thousands of years back in a legendary heroic age, about which we actually know nothing but which we'd like to imagine contains the seeds of current practice.
The MAs seem to be especially prone to this sort of wishful thinking. If people were more secure about their respective arts, there would probably be less hankering after some glorious unrecoverable past...