The OP is citing this Pew Research Report on Islam and Christianity in sub-Saharan Africa: https://www.pewforum.org/2010/04/15/executive-summary-islam-and-christianity-in-sub-saharan-africa/ but this is a subject that Pew generally takes a significant interest in--and it is a major question for scholars of African religious history and indeed the modern history of sub-Saharan Africa overall.

A good starting place might be a remark in the executive summary of that Pew report: "The survey findings suggest that many Africans are deeply committed to Islam or Christianity and yet continue to practice elements of traditional African religions". Scholars who study religion have a general name for the process by which religions combine and mix together: "syncretism". Sub-Saharan Africa is perhaps the most intense showcase of what syncretism looks like in its specifics: both Islam and Christianity have been changed by their encounter with a huge variety of traditional African religious ideas, practices and institutions, and the process of syncretic formation is still ongoing. So when you see "Christianity" and "Islam" in sub-Saharan Africa, both historically and in the present day, you need to understand right away that you might also be seeing "African traditional religion" in some form as a substantial element of practice within those two named world religions.

In many parts of sub-Saharan Africa, you might find a person who is a member of a mainstream Christian congregation also laying gifts at a shrine intended to placate a dangerous water spirit and attending a worship meeting that combines elements of pentecostal Christianity with traditional forms of spirit possession. Many people are not merely syncretic in their practices but pluralistic, e.g., they do not see multiple modalities or institutional forms of religion and spiritual belief as contradictory or incommensurable. You may have heard of Pascal's Wager, namely, that if you believe in God and He is not real, no harm done; if you do not believe in God and He is real, you're damned, so believe in God. The sub-Saharan African version might be "do all the spiritual things available to you, why not?" The one exception here might be being both Christian and Islam, because those two religions have frequently argued that they are formally incommensurable and demanded that their adherents stick to that principle. Neither religion invites syncretism with African traditional religions either, mind you, but a formal religion with organized worship is easier to mix with or run parallel to informal mixtures of rituals and deeply-seated forms of everyday spiritual reasoning.

Another element to consider is that Christianity in particular, but also sometimes Islam, have been associated with conquest, imperialism, and ruling authority. For much of the first half of the 20th Century in territories ruled by the French, British, Belgians or Portuguese, declaring oneself a Christian often opened up opportunities: access to land, access to education (particularly in the privileged European language of your colonizer), and access to professional opportunities. None of the European colonial powers invested in state-supported schooling for African children until the very end of the colonial era; almost all formal education was provided either by Christian missionaries or in parts of West and Northeast Africa by Muslim teachers, and formal education in turn was a requirement for a good deal of formal employment. Christian missions were often granted land for their mission stations by colonial administrators, and the precondition of continued residence on that land for existing communities was often at least notional or provisional conversion to Christianity. Identifying as Christian--or in some regions, as Muslim--was and remains a pragmatic or safe thing to do. Colonial officials and missionaries often treated African traditional religion with enormous suspicion and hostility, and successive waves of Muslim reformers and fundamentalists from the mid-19th Century onward could be equally strident. Meaning, inasmuch as people strongly identified as traditional religionists who strongly rejected both Christianity and Islam, they have tended to keep that identification a secret, to the point of coming to see their religious observance as characterized by secrecy. You might think this contradicts the earlier points about syncretism and pluralism, but in certain ways it actually reinforces them. You don't tell the nice interviewer from Pew or the white American anthropologist about the spirit medium you're going to see next week, just about the Methodist church you go to.

Just to try to make this more concrete using some of the examples I know best:

In southern and eastern Africa, some Africans converting to Christianity joined mainstream congregations, often headed by a European missionary. But even in those cases, elements of mainstream Protestant and Catholic worship often shifted subtly (or not so subtly) towards ideas and rituals that were compatible with or evocative of local traditional spirituality. An especially dramatic example might be the Zambian Catholic archbishop Emmanuel Milingo, who first made a splash in the 1970s by performing exorcisms and mass faith healing ceremonies. In 1983, John Paul II recalled him to Rome and removed him from his post in Zambia. (At one point he had a popular radio show in Italy, I think.) In the 1990s he became known as a Catholic dissident who was harshly critical of the existing hierarchy and an advocate of priestly marriage. He took an extra step beyond priestly marriage and actually got married (by the Reverend Sun-Myung Moon), at which point John Paul II and Ratzinger forced him into monastic seclusion for a while. He quietly left around 2004 and then in 2006 ordinated priests and bishops on his own, which was the last straw and he was excommunicated. So he's a bit of an extreme example, but a lot of formal mainstream Protestant and Catholic congregations have been pulled towards traditional ideas over the years.

Inasmuch as they refuse to be pulled (or are disciplined by their co-religionists in the same congregations elsewhere), they are also being eclipsed by more fluid syncretic forms of Christianity that sometimes don't seem very much like Christianity. Pentecostal evangelical churches, for example, are growing by leaps and bounds in much of West Africa and elsewhere. All over southern Africa, you see various groups of worshippers in public who have adopted aspects of Christian ritual like baptism but whose doctrines are often shaped far more by traditional spiritual practice--the "Apostolics" of Zimbabwe and Zambia, the "Zionists" of South Africa. Typical elements of these religious communities include avoiding pork, alcohol, caffeine or tobacco; avoiding Western medicines and medical treatment and practicing faith healing; worship ceremonies exclusively outside (you will see Zionists on the weekend in vacant lots and open spaces around major South African cities); and baptisms not just as a conversation experience but as regular purification. Adherents usually wear a white robe and they often walk together from their homes to their worship ceremonies--or sometimes gather in huge numbers together for mass worship. Many of them believe in a prophetic founding figure who is sometimes said to have been a reborn Jesus or to be directly anointed from God. Many also believe that ancestral spirits are real but essentially malign and must be rejected. Many of those congregations show up as "Christian" in the kind of surveys that Pew does but it is debatable whether that's the right label for them. (Some of the scholarship refers to them generally as "African-Initiated Churches".)

Beyond that kind of formal religious belonging, syncretic or otherwise, there are some general folk spiritual beliefs you find people following regardless of what they say their formal religious identity might be. Often these are associated with healing--many people will consult both a standard biomedical doctor or expert if they are available and some kind of indigenous healer. Many people accept that there are dangerous spiritual forces and powers in the natural world and at the command of people with malign intentions and that you have to protect yourself and understand where and when you might need to take countering steps--all without calling themselves "traditional religionists". There's a huge scholarly literature on what is sometimes called "witchcraft discourse": I particularly recommend Peter Geschiere's The Modernity of Witchcraft and Adam Ashforth's Witchcraft, Violence and Democracy in South Africa.

None of this takes away from the fact that the conversion of many sub-Saharan Africans to Christianity (of some form) and Islam over the 20th Century and into the 21st is a major change. It is. But it may be that that story is not incompatible with "traditional spirituality is alive and well in sub-Saharan Africa" (and is changing with some of the same dynamism).