Um they weren't pagan, I said Europeans called them pagan. They were mostly called pagan based on they homage to nature, by a people who were totally against nature. One of the more famous cases were akenaton of kemet who called god aton which meant 1 god. Even before him those in kemet said they came from the mountains of the moon where the god hapi dwells again the acknowledgement of 1 creator. To go even further south Africans called god ka or kai, dogan called god amma, bashango people of the Congo called god bumba, the Ashanti called god nahyamen, the ibo people of Nigeria where a lot of us are from called god chukwu which meant the first force and existence of all people. Traditionally black Africans always believed in 1 god. European invaders just came along and misinterpreted what the culture was.
Even in the bible psalms 82:6 says "ye are gods" with the plural and Jesus reiterates that scripture in John 10:34. But no one would call them pagan or polytheists. Its the same principles that black Africans understood its 1 creator but its creations as in its nature is all cumulative components of that creative force.