Zen and World War 2: http://en.wikipedia.org/wiki/Zen_at_War
Warrior Monks burning down other sects' temples: http://en.wikipedia.org/wiki/S%C5%8Dhei
Persecution and martyrdom of Christians: http://en.wikipedia.org/wiki/Martyrs_of_Japan
As to where these religious tendencies go in modern Japan, there are a number of things to think about (consider their celebrities are literally called "idols").
Confucius might not have said much about the Sky, but he constantly emphasized the importance of the Rites.
Also, once you blur out the technical theological details, is Confucius not effectively treated as a prophet? (This is a genuine question.)
In the Far East religions, you have most pieces of the jigsaw present: mysticism, the Sacred, priests, monks, prayers, meditation, afterlife, etc. But I think the central piece of a unique almighty exclusive God is missing, and then the result is completely different.
There is also this theory that the Far East did not have a powerful scientific revolution because of this missing piece: Without a God who created everything, there is less incentive to believe in a unique ordering of things (the Law of physics) and to try to discover it.
And no, Confucius is not a prophet, he made no miracles, he did not announce anything. He was just a failed political advisor who became the teacher of a few disciples. However, he proposed a very rational and revolutionary way of life, under the disguise of restoring the ancient Way. He also happen to be (along with Jesus and maybe Mohammad) the man who influenced the most the lives of most other humans.
The Japanese did some horrific things in the name of their Emperor, so I don't buy your assertion.
You could argue that the Far East are simply religiously backwards, using polytheism instead of monotheism, so your argument actually makes no sense, they simply haven't caught the monotheistic religious bug (yet).