The answer to this question can be found in Chapter 19 of Guns, Germs, and Steel. There, Diamond explains how Africa came to be dominated by Bantu people. Among those who were displaced from their lands were the Khoisan. Diamond speculates about what became of their “vanished populations” beginning on p. 396.
Because we have no direct evidence of what happened to the Khoisan populations in the areas that the Bantu took over, Diamond tries to project what happened to them based on the experiences of other hunter-gatherers who were confronted by invading farmers in historical times. He looks at the experience of the Aborigines in Australia and the Native Americans in California to give us an idea of what happened to the Khoisan. On p. 397, Diamond gives his fairly grim assessment of what happened to the Khoisan. He speculates that they
were rapidly eliminated in a combination of ways: they were driven out, men were killed or enslaved, women were appropriated as wives, and both sexes became infected with epidemics of the farmers' diseases.
In these ways, the Khoisan disappeared from the lands that the Bantu wanted and were able to take. Of course, Khoisan populations continued to exist in marginal lands that the Bantu did not want and in the southernmost part of Africa where the climate is not suitable for the Bantu’s tropical plants. So, the Khoisan did not all die out, but their vanished populations were either killed or absorbed into the Bantu population through slavery or forced marriage.