An alternative explanation would be that those records weren't kept with any kind of care and the current authorities can't say either way.
The Marshalls are pretty far away from Japan, and so were cut off pretty early. They were also the site of heavy fighting (unlike, say, most of what is now FSM) so it's easy to imagine paperwork preservation wasn't a high priority.
The Japanese also treated prisoners quite horribly during WW2. I doubt records were even kept of every civilian that was killed, especially if that person gave no indication of being significant.
I discovered the story originally while absentmindedly Googling about Earhart a few months ago (when I can't sleep I read about curious historical mysteries; Black Dahlia, DB Cooper, etc. Then I have a harder time sleeping!).
The Marshalls are pretty far away from Japan, and so were cut off pretty early. They were also the site of heavy fighting (unlike, say, most of what is now FSM) so it's easy to imagine paperwork preservation wasn't a high priority.