I think it's unusual for people to be openly gay, as it's a personal matter. For that reason, it's not easy to say exactly how rare it is, but since Japanese are human like the rest of us, you could expect homosexuality to be about as "rare" as it is in the US or anywhere else. A trip to Shinjuku 2-chome would help illustrate this point, and show that there certainly are homosexuals in Japan, and in the right venue, are quite open about it.
But is this what you are asking about, or are you asking about affectionate friendships between people of the same sex (like bosom buddies?). This is not homosexuality.