How is the designer of a plane a war criminal? The fact that he designed an a pretty good airplane makes him a amazing person in itself. And for Japan he would be quite a hero. And the term 'war criminal' is used for a completely different case. It refers to person who take advantage of the war in order to satisfy their own personal needs. Like for example, you took advantage of the war and robbed/murdered your neighbor since everyone was busy and no would care what you would do at that point. Something like that.
In all sense, the designer of the airplane or the atom-bomb for that matter cannot be considered war criminal's. Sure you might not like them, hate them even, but they are definitely not war criminals. And I don't see them being glorified a problem. Each person his/her provided their own country with the means it required. The person who would authorize to use them, a totally different thing.