Did they know of it? Yes. Christianity has been in Japan since 1549, possibly even earlier but the arrival of Portugese missionaries is the first we know of for certain. In either case, it's been in Japan for centuries and Imperial Japan was most certainly aware of it and what it was. Even though the christian population of Japan was always small several prominent politicians were openly Christians, perhaps most famously so in that era Takahashi Korekiyo who had served as both prime minister and minister of finance. He was responsible for securing foreign financial support for the Russo-Japanese war, abandoning the gold standard, funding much of Japan's build-up through significant deficit spending etc. Definitely a well known person in Japan. Somewhat ironically he was assasinated by the imperialists in 1936 for wanting to cut government spending.

In either case, yes, the Japanese were certainly well aware that Christians existed and that almost all of their western enemies were christian, this wouldn't have come as a surprise for anyone. Many high ranking Japanese politicians and officers had studied, lived or worked in the west, generally the US or Britain as Japan had relatively strong ties to both nations until relations rapidly deteriorated in the years leading up to the war. Generally speaking POWs were allowed to hold services in camps (although conditions were generally speaking atrocious, not making excuses for the IJA treatment of POWs here).