Actually, there is a way that such offspring could exist without the need for magic, shady drugs, Yukari fooling around or futa, and that is simply due to Gensokyo being a land of illusion.
Think about it: things happen and exist in Gensokyo due to them being actively disbelieved or disproved in the outside world. Here, we know as a scientific fact that homosexual intercourse of any kind will not yeild any offspring, and because of that, there is the chance that in Gensokyo, it could. Therefore, one girl could theoritically get another girl pregnant.
...Or maybe I'm just a rambling lunatic.