It’s somewhat funny how shamans may date back to the Stone Age; while, pagans, and witches disappeared with the rise of Christianity and Islam. I suspect most consider shamans as generally male and witches as generally female; which, may play a role in the surmised death of witch cults and paganism, but you also have to consider the religious ties of shamanism — does a shaman need to believe in God or just the power of mushrooms and other hallucinogens found in nature?
I’ve written two unpublished novels about a fictional witch/fertility cult and I theorize such a cult could survive. Wikipedia has an article called the Witch-Cult Hypothesis and skepticism surrounding the survival of such a cult, but take note how Jewish Mysticism (the Kabbalah) survived; thus another form of mysticism survived. Isn’t there a similarity between mysticism and witchery? Is a witch much different from an alchemist or a shaman? Do the pheromones found in perfume differ much from a love potion from a theoretical witch? Theoretically, perfumery was an ideal place for witchcraft.
The term crypto-pagan would apply to pagans hiding among Christians, Muslims, or even Atheists. Such people would have needed to hide for over 5,000 years. In the 16th century, interest in mystic arts began to arise and the invention of the printing press broke the Vatican hold over religious view in the Christian world. I theorize Gnostic Christians could have hidden within Inquisitional Catholicism and bring with them many pagan concepts. Catholic saints often share aspects of pagan deities and many pagan symbols became part of the Church.