1. Not something I have specifically studied, but a complex set of factors from the increasingly harsh discipline within the Army from the 1920s effectively brutalising soldiers along with propaganda, to complex psychological issues like obedience to authority.

Really there is no simple answer to the question that I can give is to suggest some reading - Yuki Tanaka's Hidden Horrors, and Meirion and Susie Harries' Soldiers of the Sun might be some good starting points.

2. A mix of actual and assumed knowledge. The majority judgment of the IMTFE viewed massacres of civilians, PoWs and wounded and sick as having been ordered by officers or those higher in the hiearchy [Judgment 49643-5], and that massacres were a matter of policy where it was thought best to do so to capture resources intact [49631-3]. In the case of the executions of Allied aircrew, there was a finding that Tojo at least had signed off on the executions. There was found to be direct authority to use PoWs in war production and orders to execute attempted escapees (both breaches of international law).

However in many cases, the evidence prosecutors had did not clearly establish orders (if these ever existed, they were potentially destroyed) and so utilised the legal concepts of command responsibility. The indictment made a count for "order[ing], authori[zing] and permitt[ing] war crimes (Count 54), and a separate charge of "deliberately and recklessly disregarding their legal duty to take adequate steps to secure the observance and prevent breaches thereof" on the basis of their office or position having a responsibility for making sure the laws of war were observed. There was also sufficient evidence from various government meetings to show that war crimes issues came up and were discussed, including ones where Hirohito was present.

Essentially, where they were unable to show a direct order, the argument was that they had failed in their responsibility to ensure atrocities did not happen, and thus were responsible. This included where they were understood to have information about atrocities and done nothing about them, or had done something but failed to do enough.

Overall, war crimes were both - in some cases there were official policies and directives to do (or not do) things amounting to war crimes, or deemed negligence of responsibility to ensure they did not occur. In some cases atrocities occurred as a result of decisions of troops on the ground and commanders either effectively approved them by doing nothing or in some cases were not in a position to stop them (Yamashita in the Philippines 1944-45 comes to mind, some argument perhaps in the case of Matsue Iwane at Nanking in 1937). For the most part though when war crimes occurred it was because they were specifically ordered or the leaders were not concerned that they were occurring. This did not mean they necessarily approved of the action, rather they did not care.

There are of course many reasons that an individual might take part in atrocity; profit, fun, adventurism, psycopathy. However, for the purposes of this question, the two most common answers would be (1) common beliefs of racial superiority, and (2) cultural shame placed on surrender.

In terms of racial superiority, the rhetoric in Japan at the time was one which saw the Japanese as a superiour race, especially with respect to the Koreans, Chinese and Filipinos in the areas that they conquered. This led them to commit abuses against civilians rivalled only by those commited y the Nazis in Eastern Europe. The occupation of Nanjing (or Nanking) is often reffered to as the “Rape of Nanking” with as amny as 300,000 killed and 20,000 women raped. Also infamous was the Unit 731, which conducted tests of chemical and biological weapons reminiscent of Dr. Mengele’s torture of inmates at Auschwitz.

Secondly, the cult of bushido placed a large amount of shame on surrender in combat. Japanese soldiers were expected to fight to the death, with surrender not considered an option. At the Battle of Iwo Jima, of a force of 20,000 Japanese soldiers, only about 200 chose surrender, with the rest fighting to the death. The Geneva Conventions, and the idea that those who surrendered human treatment, was completely foreign to the Japanese Imperial military at the time. Because of this, allied soldiers who surrendered (regardless of whether they were British, Canadian, Indian, etc.) were worked to death The Nazis, by contrast, merged from the European culture in which killing an unarmed soldier is seen as dishonourable, leading them to treat prisoners from the Western front surprisingly well. This was not the case for Soviet prisoners, deemed ideologically corrupt and racially impure as Communist Slavs.

A better explanation, I would argue, than either racism or culture, would be the idea that military-authoritarian bureaucracies are a metaphorical bad barrel which create and encourage abuse regardless of racism or culture. Christopher Browning’s book Ordinary Men makes this argument far better than I can, where he demonstrates that the worst abusers in the Holocaust were not racists or idealogues, but rather were literally ‘ordinary men’ following orders.

In terms of the second question, the International Military Tribunal for the Far East (also known as the Tokyo Tribunal, the Pacific theatre’s equivalent of the Nuremberg Trials) demonstrated quite clearly that the majority of the Japanese high command were guilty of organizing crimes against humanity (referred to as ‘Class C’ crimes).

It seems doubtful that the Emperor didn’t know about the conduct of the soldiers and the abuse committed by them, as the level of devastation was too widespread and commonly known. The Americans decided to leave him in power more due to pragmatic reasons, since the Emperor wasn’t as hated a figure in the West as Hitler was, and because they were worried that convicting the emperor would create more conflict within Japan. Since the Americans wanted allies against the Soviets, it seemed better to leave Hirohito in place and recruit the Japanese to the American sphere of influence.

EDIT: spelling mistakes

EDIT: I was asked to add a short bibliography. Here it is:

Browning, Chistopher (2001). Ordinary Men: Reserve Police Battalion 101 and the Final Solution in Poland.

Chang, Iris (1997). The Rape of Nanking: The Forgotten Holocaust of World War II.

Totani, Yuma (2009). The Tokyo war crimes trial: the pursuit of justice in the wake of World War II.