(i) Japan could now be trying to reduce its $ holdings without offending the US, or (ii) someone high up in Japanese banking or politics might have purloined them in the past. The sums are huge, so I would have to go with the former explanation.
But if they were legit paper, truly owned by the BOJ or the government of Japan, they could have been shipped in a diplomatic pouch and avoided all of this nonsense and been truly discrete.
That’s the first, biggest reason I have problems believing these are legit: If they were legit, the amount is so large that no one other than the Japanese government could have owned US bearer bonds from that era other than US citizens and US banks. The only off-shore nation buying up that amount of debt back then was the Japanese. So that much fits.
But if they were buying bearer bonds, they as a government enjoy the perks of diplomatic relations, which include diplo pouches. Japan could have couriered the paper to Berne and been done with it.
I will readily admit that Japan’s recent statement of confidence in the US in context of this seizure is quite odd, however.