/jp/ - Otaku Culture

http://en.touhouwiki.net/wiki/Perfect_Memento_in_Strict_Sense/Divine_Spirit

>Divine spirits, not possessing a body, usually live in a Shinto shrine or in a smaller shrine

>There is a considerable lack of spirits in a shrine, so revealing their forms to people is something that mostly never happens. They speak so faintly that ordinary humans can't hear them. For this reason, those who carry the duty of facilitating communication are shrine maidens.

If you read the whole article, you can see that divine spirits are basically the same thing as a god, at least in the shrine living/faith business.

It's very likely that Reimu's shrine actually hosts a divine spirit, one that is responsible for the foundation of Gensokyo. The above note also explains why we never get to see it, plus, _we_ barely ever get to see Reimu alone inside the shrine, since Marisa has the compulsive need of having to stay within 2 feet of Reimu about 95% of her lifetime.