According to Larson and Faust, Bat Ponies are a separate type of Pony who live in caves in the mountains, but since Equestria is all about The Three Tribes, it makes sense that they would be a race of Pegasi who just adapted to semi-underground life; if thats the case, its not much of a stretch to assume there are also dark-adapted Unicorns and Earth Ponies as well, and I like the headcanon that converting above-ground Ponies to their underground versions is something Princess Luna can do for volunteers.