Having your bags taken and put into checked luggage happens everywhere, if the plane is full and you are one of the last to get on. If you want to avoid it, make sure you get a seat at the back of the plane and as far as possible, try to get on the plane first.
The problem is that many people take too much stuff with them as carry on luggage, the plane fills up and there is no where for the late people to fit what they have. This is especially true in Africa. Also, SAA tends not to board by rows, it is just a case of everyone get on. So don't show up at the last moment.
As a rule of thumb, take one bag, preferably a small backpack. You probably wont have any issues then since (if there is any argument) you can fit it under the seat.
Otherwise, if you don't want to do that and still bring a small arsenal of equipment with you, fly a different carrier. SAA is not the only airline to fly to South Africa.
You might want to do that anyway even if baggage is not a problem, since SAA cabin crew have got to be among the worst out there. They are among the most unfriendly, sour and unhelpful flight attendants I have ever encountered. They all seem to hate their jobs, or more precisely, they like having the job and the travel it brings, but hate the actual doing it part. It could be that most of them are black, whereas most travelers on SAA flights are white, and there is some carry over resentment from the apartheid era where they see catering to the needs of a bunch of white folk as demeaning. In any event the general attitude of their flight attendants is very sullen.