So my take on this for the time being is as follows; Amazon.com has had trouble maintaining its usually high-level of service to South Africa for the same reasons most other international companies do - we are far away from the developed world. Getting things to and from South Africa from places as far afield as the USA is challenging and processes are unreliable. The reason this isn’t the case in the rest of Africa is simply because no other country on the continent offers anywhere near the amount of business to Amazon as South Africa does.
I think the real reason Amazon.com doesn’t want to ship to South Africa is because it would prefer to divert all business to the region via its UK presence. And yes, that has something to do with “lost” mail, but not everything.
