The 1936 memo that Hirohito approved which expanded Unit 731's operations was part of a larger Kwantung Army expansion. The memo notes that the so-called "Kwantung Army Epidemic Prevention Department" and the "Army Horse Epidemic Prevention Department" needed to be expanded. There were few, if any details, as to the true extent of the project. As it was, central government control of Kwantung Army actions was more or less non-existent.

On the other hand, several of the Emperor's brothers, including Prince Mikasa, toured Unit 731's base of operations, and saw a video of Japanese planes being loaded with plague bombs to be dropped on Chinese cities, as well as one where Chinese prisoners were tied to poles and had poison gas dropped on them. 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.

I would argue that it is safe to say that Hirohito was aware that at the very least, chemical weapons were deployed in China.