This seems equivalent to hypothesizing that "their wallets may have been lost due to their harddrives crashing." Sure, it's possible. But it's easy to come up with dozens of possible theories.

What evidence do you have that the US government has done that against Japanese companies in the past?

(Mt. Gox may have had a US division, but they were a Japanese company, not a US company.)

EDIT: Also, if the US had seized most of the coins, why would they suddenly have a change of heart and allow Mt. Gox to release 200,000 BTC?