Went around 2000...stayed in Cape Town 1 night then flew to Johannesburg then on to Windhoek, Namibia. Hunted with Jan Oelofse (my grandpa was great friends with Jan). The only warnings we had were to stay in our Hotel after sunset in Cape Town and avoid anyone asking for money...which was about every 5 minutes while on the streets. Razor wire around courtyards or houses was the norm but never really felt unsafe. Once we were "in the bush" zero concern. As others have said the reputable Outfitters/PHs have a pretty darn good system down and live it everyday.
It was a treat listening to the stories of when my Grandpa first started going hunting in Namibia on Jans place during the Namibian wars. They were escorted everywhere by a small military guard and every day the perimeter was inspected for any sign of intrusion by other humans. Besides those early days my Grandpa has been to Africa 8 times or so...even in Tanzania right after the 1998 embassy ordeal and has had zero issues.
Been across the pond 6 times (both hunting and travel) and hopefully headed back next summer. Had 4 different friends hunt in SA over the last several weeks and not an issue. South Africa is definitely the more modern of the Southern African countries. Prices for some plains game are quite cheap compared to years past. For the cost of a guided elk hunt you could take 5-6 animals and live large.