Because the IRL societies which did spend time and effort considering the spirits of nature, were not literate. They didn't leave their own records to study or use as inspiration for D&D Sourcebooks.
We do have some Roman records and some Age of Exploration -era records to work with, which (alas for your purpose) are written from an outsider's viewpoint.
Conclusion: learn what you can, and think about it. Then make up what you have to.
Look to Asia. Thai buddhism is to this day filled with traditional animist beliefs, as are other minor religions and folk traditions. Animism is not gone.