As far as the exclusion of Japanese sexual atrocities in particular goes--basically, nobody likes to think (much less write) about rape, and it adds an extra layer of horribleness to the story that's hard to deal with, both emotionally and as a writing problem--how much PTSD should victims display? Did any of them get pregnant?
@Ross also points out in a comment that "Japan's rapid postwar westernization and our own atrocities in the form of two atomic bombs has softened our judgment of it, in comparison to Germany," which is a good point that I didn't originally consider.
The TV show
They sort of address this in Season 2 (I posted the question after watching Season 1). Juliana is hitchhiking with a man who was a medic in a MASH during the war, and he says:
I like to use this road if I can. It's good to be reminded. A few miles that way, there's a redwood grove where they all went near the end, waiting to surrender. We set up a hospital, put boys back on their feet that had no business breathing. Then the Japs came through. Lined them all up. Women and kids, too. One bullet each to the back of the head. Never more than one. Took about an hour.
This isn't much, but it's about as much screen time as they give to Nazi war crimes. (I'm not counting the peacetime terrible-ness of the Nazi government, which as far as I know doesn't really have a Japanese counterpart.)
You can take the part in Season 1 Episode 6 when the hiring manager in the Nippon Building demands "personal services" from Juliana as a subtle/weak nod to the comfort women, if you like.
Here's an interview with PKD in which he says:
And that’s why I’ve never written a sequel to it. Because it’s too horrible. It’s too awful. I started several times to write a sequel to it and I would had to go back and read about Nazis again. And I’d just like to off every one of them, it’s what I’d like to do. And so I could never do a sequel to it.
I found this via the quote in Rand al'Thor's answer to Will there be more of "The man in the high castle"? and thought it might apply to the Japanese as well, but if you look at a longer quote (emphasis mine), it doesn't:
Phil: ... When I sit down to the typewriter I’m going to know what I’m talking about. Man In The High Castle, I did 7 years of research for Man In The High Castle. Seven years of research. I did other stuff too during that 7 years. But it took me 7 years to amass the material on the Nazis and the Japanese, especially on the Nazis, before I could sit down and write. That’s part of the reason why it’s a better novel than most of my novels, that I knew what I was talking about. There wasn’t anything I didn’t know. I had prime source material at the Berkeley Cal Library from the Gestapo that they had seized after WW II. It was marked, for the eyes of the higher police only. The higher police is their term for – I was forced to read Gestapo diaries, the Gestapo men in Warsaw, Gestapo agents. I had to read that stuff. I had to sit there because you couldn’t take it out of the library. You had to read it in the stacks. I had to read what those guys wrote in their private journals to write Man In The High Castle. And that’s why I’ve never written a sequel to it. Because it’s too horrible. It’s too awful. I started several times to write a sequel to it and I would had to go back and read about Nazis again. And I’d just like to off every one of them, it’s what I’d like to do. And so I could never do a sequel to it. Somebody would have to come in and help me do a sequel to it. Someone who had the stomach for the stamina to think along those lines, to get into the head; if you’re going to start writing about Reinhard Heydrich, for instance, you have to get into his face. Can you imagine getting into Reinhard Heydrich’s face? Now, Condon, Richard Condon, is that his name, he wrote a thing called An Infinity Of Mirrors about Reichfuhrer Himmler. Condon has the guts to do that. I could not do that again. That’s why the book, my book The Man In The High Castle is set in the Japanese part, you see, because then I could deal with people. But I have little glimpses of the Nazi part like when Mr. Tagomi hears this printout on personality traits of the Nazi contenders for Reichsfuhrer, Reichs Chancelor, I’m sorry. And he runs out and gets sick and falls down.
Mike: That was you.
Phil: That was me. That was me. Horrible, he said, horrible.
From the longer quote, it's clear that PKD does not see the Japanese as too horrible to write about, and in fact identifies with one of the Japanese characters himself. It's not clear to me why this is--perhaps it's just due to what materials the Berkeley Cal Library happened to have.
I did look into the history of discovering and publicizing Japanese war crimes. Many of the perpetrators were tried publicly soon after the war. Per Wikipedia:
Soon after the war, the Allied powers indicted 25 persons as Class-A war criminals, and 5,700 persons were indicted as Class-B or Class-C war criminals by Allied criminal trials.
"Class A" crimes were reserved for those who participated in a joint conspiracy to start and wage war, and were brought against those in the highest decision-making bodies; "Class B" crimes were reserved for those who committed "conventional" atrocities or war crimes; "Class C" crimes were reserved for those who committed Crimes against Humanity. This includes murder, extermination, enslavement, deportation, and other inhumane acts committed against any civilian population or persecutions on political or racial grounds.
So we've got the 5700 people tried for war crimes and crimes against humanity soon after the war; I believe this figure does not include the defendants of the Nanjing War Crimes Tribunal at which General Yasuji Okamura testified:
First, it is true that tens of thousands of acts of violence, such as looting and rape, took place against civilians during the assault on Nanking. Second, front-line troops indulged in the evil practice of executing POWs on the pretext of (lacking) rations.
I don't really see how PKD could have failed to notice any of this in seven years of research, and if he did, I don't understand why he chose to portray Japanese imperialism so positively.