For reasons having to do with current events elsewhere in Africa, Johannesburg does seem to be the best bet this time for legs in Africa. (Uganda, Rwanda, Congo involved in conplicated civil war conflict, Sudan/South Sudan situation still unsettled, etc.
The question I have is whether all of the remaining teams would have to go through Hong Kong to get to Johannesburg; or whether teams leaving Hanoi could have gone to Singapore, Bangkok, or other hubs to get there. If we haven't seen all of the teams at the Hong Kong airport, then the other question is whether the teams that were seen there are leading or trailing teams, or risk takers or risk adverse in their travel arrangements.
The other comment I'll make is that South Africa as the next country is still consistent with a mostly-southern hemisphere, or at least south of the Tropic of Cancer route that I've been speculating about.