On the original question of security of luggage at JNB, it is normal now (same as at SYD, for example). In 2003 or 2004 a big luggage theft ring was broken up at JNB (dozens of airport employees arrested) and this solved half the problem. The other half was from non-airport employees and this was subsequently solved, in part with a big and very visible police presence (patrolling the terminals and airport grounds). JNB has made a concerted and diligent effort to solve the crime problem at JNB and has been successful.
As for the rest of the country, it varies from charming and wonderful to hellish. There are some areas where you do not stop the car under any circumstances (not even for red lights, called "robots" there); in fact the law was changed a decade ago to make it legal to run red lights under some circumstances. Those areas are rare, but you need to know where they are before you drive around on your own (or just stick to routes that you have cleared with locals in advance, e.g. your hotel concierge).
This can be one of the best countries in the world for a tourist, but parts of it is also the most dangerous. The large dichotomy can catch some people off guard.