There's a lot going on here. Basically, your girlfriend is dead wrong. As for her complaints about America and Hiroshima - she really has no place complaining to a Chinese-American about WWII war crimes if she is also refusing to say a critical thing about Japan. For obvious reasons.
But each of her comments can be countered very easily - nothing she talks about is without its negative side. She has a severe case of "rose-colored glasses." You've mentioned her talking about samurai culture and traditions, which shows she has very happily "drunk the Kool-Aid" when it comes to Japan's national myths. And that's exactly what's happening here: she's repeating national myths to you. Myths. There are some grains of truth to what she's saying, but she is not telling you, nor does she seem to know, the whole story.
Take 1) Japanese people are not mindful. Period. Well-mannered? When they have to be. They also tend to get drunk and vomit in public.
2) A lot of crime goes unpunished here because the cops ignore it - stand at any intersection in Japan for ten minutes and you'll see dozens of crimes. There is hardly any enforcement of traffic laws here. There are plenty of other things that the cops happily ignore. For example, gambling is technically illegal here, yet Japan has some of the highest rates of gambling addiction in the world. How is that possible unless people are committing crime en masse while the police watch? Sexual crimes, such as groping and flashing are well-known to be common here. There are some serious criticisms to level at the police here. Japan is certainly non-violent, but law-abiding? I personally do not consider people law-abiding here.
3) Healthcare is in no way, shape, or form free in Japan. Your girlfriend is either flat-out lying, or she has no idea what she is talking about. You not only pay for national insurance, you pay out of pocket for all medical procedures. Many doctors charge you massive fees for literally nothing, and there are plenty of other serious criticisms to aim at doctors.
4) The food in Japan is not qualitatively better or fresher - it is, however, heavily tariffed and taxed. All food is expensive, and there are high tariffs on imports. Choices are limited here, far more limited than they are in the US. You pay more and get less. I used to be able to buy fresh raspberries at the grocery store in America. In Japan? I haven't seen raspberries in years.
5) Nothing about this comment is really true or untrue. Some people are polite, some are not. Score one for your girlfriend, I guess.
6) Service in Japan is fine, but store clerks here will often look you in the eye and say, "No" if you ask for something special. People do put on a good show, but it's common for Japanese store clerks to flat-out refuse, unapologetically, to go out of their way to help you. Not even getting into how some will refuse to even talk to you if you're an immigrant.
7) This one pisses me off. Each of her comments has a grain of truth to it - but this one is just plain old bigotry.
America is known around the world for charity. We have charity unlike anything in Japan. In 2013 or 2014, America took in 60,000 refugees and gave them safe places to live. In that same time period, Japan took in six. Fucking six. I've personally volunteered with some of those refugees. Japanese people are the absolute last people on the planet to give Americans shit about helping people.
Japan is a nice place, with actually very good social safety nets. I know, my wife has used them, and they have helped us even after our marriage. But actual charity? Japanese people cannot touch America for charity.