I would be suprised if the Japanese govt was actually involved. If so they would have moved them via diplomatic pouches which are not subject to search as I understand.
More likely they are either privately held - unlikely; stolen - plausible; or forgeries - probable.
Still it does make for interesting conjecture and either way would represent a serious risk.
Why forge them? Who would take a $500 million bond except a huge bank which would verify them first.
One problem with their being forgeries: there is NOBODY who is going to cash a $500 million face-value bond who will not verify it's authenticity with the US Treasury before handing over the cash. And bonds are serial numbered.
If they are stolen, you would expect that whoever they were stolen from would notify the US Treasury (unless it was really big time drug dealers).
All in all, an impressive mystery.