Sure, but look at the larger context-- those two pieces of media first and foremost are anime which are where more of Japan's risque takes occur. Barefoot Gen was made by Madhouse, which was an extremely new studio at the time. These aren't live action movies made by some conservative, pre War joint stock company like Toho. Cold War 198X also has nuclear war depicted in it accurately from a military perspective, but again, it's anime.

And yes, it's the same in the United States. There are plenty of films that criticize the US government or elements of it. In the 1950s, there were Westerns which did it. In the 70s and 80s, there were Vietnam war movies which did it. Post 9/11, you have Snowden-related movies, or even movies like Captain America 2.

However, yes the DoD offers many incentives for portraying US weapons systems as cool, or US forces in a positive light to "content" makers (I hesitate to call them films).

As Japan rearms to face China, and seeks to boost recruitment we will see more of this patriotic attitude. And maybe Godzilla will be China one day.

(It's hilarious, because in China's recent Korean War films, the United States is scarier than Godzilla to their troops who spend 80% of the movie running away and dying).