Although I love day flights, they are inconvenient if you’re not flying point to point. In the case of KLM to CPT and JNB and Edelweiss who fly a once a week day flight in the European winter months, you have to stay overnight before flying on and in my case before flying out as well. This makes for a very long journey and adds to the cost.
Swiss use the opportunity to do a full deep clean of their planes while they are sitting on the ground at JNB and others do maintenance, so it’s not time entirely wasted. Must also not forget that when a plane sits its not costing money in terms of engine and airframe use either.
I know QR fly to CPT and Maputo via JNB and I think TAP also goes via Maputo. Other than that every European and ME carrier I can think of, including EK, IB, AF all sit at either, or in some airlines case, both JNB and CPT the whole day.