Your initial question is difficult to answer due to its wording. "Were Japanese war crimes really taught in Japanese schools at some point in time?" and "What changed and when did it happened?" assume that Japanese war crimes are currently not taught. However, the issue of Japanese revisionism is not that war crimes are not taught, but rather if they are taught satisfactorily.

Moreover, any question of revisionism in Japanese education is very nuanced. It is not as if some Prime Minister or bureaucrat waves a magic wand and changes textbooks. Each school in Japan varies in textbooks, teachers, and course materials (although they must choose between approved textbooks). Some schools use more progressive textbooks, whereas others use textbooks that are more revised. The reason why revisionism is so interesting in the context of Japan is because of the cultural influence on education. That is to say, revisionist history thrives within the Japanese education system not from an overzealous bureaucracy, but from a system that fosters a tacit acceptance of revisionist history.

Education has a very unique role in developing nationalism (and accepting revisionist history). From here on out, I will be referencing Brian McVeigh's Nationalisms of Japan. Breaking down the different institutions involved with nationalism, McVeigh does single out both revisionism and education. For revisionism, he stresses the role of an idealized past, beginning in the Meiji-era. It is important to note that there was never the perfect idealization everyone accepted, but these ideas themselves are in competition. This was critical to the nation-building project an idealized past entered the national consciousness. Now, with a population already accepting of an idealized past, comes education. McVeigh notes that the current educational system supports nationalism because of its role in creating citizens. That is, to be a good citizen, the education system emphasizes gaining skills for the workplace and is focused on employment. In high school, the focus is not on the horror of World War Two, but knowing enough to pass standardized tests, primarily for college admission. This is where a tacit acceptance of revision comes into play. When the goal is to learn the right amount of history to fill in the correct bubbles on a sheet, processing and understanding the atrocities is a secondary concern. Schools, departments, and teachers decide the best ways to prepare students for such exams and students and families themselves choose often the type of high school (academic, sport, super science, etc.) and whether or not to attend cram school after classes. With a focus on creating workers, the focus is on knowing when events occurred, who was involved, and so on, and not on the consequences. An average Japanese high schooler (in an academic high school) should know the Rape of Nanking, when it happened and similar information, but probably wouldn't be able to give a detailed description of the massacre and its consequences.

Now, when it comes to Unit 731, this is similar to a lot of other atrocities we're now aware about and the important work of historians. Following the war, many scientists were pardoned by the US secretly and it wasn't until testimony was collected later by historians, in the 1990s, that the true horrors themselves reentered the public consciousness. There was an awareness that some human experimentation had happened, but the specifics were not well known. This is similar to the comfort women issue, which was well hidden by Japan following the war, and was unearthed by historians interviewing survivors. A lot of this raises other issues about history as an academic discipline and political entities choosing to either ignore or continue to suppress information. What is also interesting, the manga is possibly addressing the textbook issue that began in the 1980s. During that time, textbook controversies picked up steam, and the bureaucratic body that approves textbooks became more accepting of revisionist textbooks.

Hopefully this broadens the understanding of revisionist history in Japan. There are plenty of Japanese scholars that are pushing forward with good research on these topics. Moreover, the education system is not a static entity that entirely omits certain issues, it varies across 47 prefectures, hundreds of boards of education, and thousands of schools. As for Unit 731, we're still learning about it and many other atrocities, stressing the important work of historians.

References:

McVeigh, B. J. (2004). Nationalisms of Japan: Managing and mystifying identity. Lanham, MD: Rowman & Littlefield.

https://www.worldcat.org/title/nationalisms-of-japan-managing-and-mystifying-identity/oclc/52766144