I was there in Sept of 2017
In Cape Town I didn't have any problems flying except on top of table mountain.
I flew an entire battery of my mavic pro and when I brought it back to me, on security guard came over and said I can't do that here.
that I can get a fine. so I just told him, I didn't know that Im so sorry, and he was cool about it. I was able to keep the footage too.
other than that I was every where with it. I even flew it off a boat while I went great white cage diving. got permission from the captain and he was super cool about it.
In limpopo near Johannesburg we also stayed at a wildlife reserve where the resort was in the safari with the wild animals. (2 weeks prior to us getting there a cheetah hunted and killed a kudu infront of the reception entrance. super cool) but it was super safe.
They told me No I couldn't fly the drone because of the safety of the Rhino. Theres such a bad pouching problem with the rhinos that they didn't want any drones in the air. which I respected. we were even asked not to tag any of the rhino photos or video with the reserve we was at. they didn't want the poachers to know how many rhino live there.
As long as you ask for permission and your granted with it you can fly over their property. I never had any issue except for the top of table mountain.
Hope this helps. you can see some videos I took in south africa on my youtube channel to see where I've flown.