Oddly, while the "why was Emperor Hirohito allowed to stay in power?" question gets asked quite often (here I am linking to some posts two weeks ago), the "which atrocities did he know about?" question does not as much, but there are some past threads of interest:

This thread specifically asks if he knew about Unit 731, with observations by /u/ParkSungJun. An excerpt:

In an interview with the Yomiuri Shinbun, Prince Mikasa mentioned the video, noting that he had to cover his eyes in disgust at the atrocities. It is very unlikely that Prince Mikasa did not tell Hirohito any of this.

Then again, many military officers had no compunctions in hiding information from the Emperor: Hirohito had no idea what the situation in Guadalcanal was, for example, until at least several weeks after the commencement of the operation.

This thread by /u/Lettow-Vorbeck discusses how he rubber-stamped what the military put in front of him.

Certainly, the military acted not only without the civilian government's co-ordination or even knowledge, but the army and navy would act without each other's co-operation. Moreover, the army had many radical officers act on their own accord to start wars and coups in China. The take over of Manchuria was done against the express wishes of Japan's state department, by officers lower than the rank of general. Furthermore, the Marco Polo bridge incident that sparked the Second Sino-Japanese war was started by local military commanders' overreaction to a missing soldier. All of this mess needed to be filtered through military commanders that were tied to that mess and over to Hirohito.

Hirohito did know about many of the atrocities, and failed to act to stop them. There is evidence of him expressing regret for the war, which implies guilt. However, people should know that he could have been replaced, and almost was by calling for peace...

Finally, here is /u/kieslowskifan discussing a controversial book by Herbert Bix.

On an abstract level, Hirohito does make a compelling argument that the Japanese emperor was willing to go to war on the cheap and signed off on a number of policies that escalated the conflict within the East Asia into a truly global world war. The popular image of the emperor as a genial man out of his depth who only wanted to be a marine biologist is one that really does not really fit the existing evidence.

A great deal more can be said about the matter, so new answers are very welcome.