Right!
The 99% globetrotters win! [
Flat Earth Theory.]
Johannesburg to Sydney flights. If 1% of the supposed flights take that direct route, why would 99% take 1, 2, or even 3 stops, detours; taking two, three times longer and costing more? They must be as dumb as the Flat Earthers! ...or
Because of economics, the physical limitations of aircraft, global aviation safety regulations and the laws that control international air travel (as embodied in the Chicago Convention).
Here's a quick explainer on legal side.
All international flights require the permission of multiple governments to operate. At the minimum, you need the departing and arriving countries to give permission. If you operate a stop via an intervening country, you'll need their permission as well. And different permission if you want to pick up/drop of passengers at the intermediate point(s).
These permissions are (typically) given under bilateral (two party) air services agreements (ASAs).
If you want to operate South Africa-Australia, you need approvals from both governments to operate the route. Usually, one of the stipulations is that a carrier is 'flagged' (that is, effectively owned or controlled) in one of those countries.
But, what if you want to operate South Africa-Australia and you're not a South African or Australian airline? Well, you can still do it, via what are known as fifth and sixth freedom traffic rights.
So, if you're Emirates and you're owned by the Emirate of Dubai, you'll have bilateral ASA rights to operate Dubai-Sydney-Dubai under Flight A and and you'll have ASA rights to operate Dubai-Johannesburg-Dubai under Flight B.
For legal purposes, those are technically separate flights under separate ASAs between pairs of governments. But, for commercial purposes you can combine Flight A and Flight B under a single ticket sold at either end and turn it into a Sydney-Dubai-Johannesburg route (or Johannesburg-Dubai-Sydney).
This is how a LOT of long haul travel operates - through large transit hubs. The big ones for international connecting traffic are Singapore, Hong Kong, Dubai, Doha, Abu Dhabi, Panama, as well as some more traditional point-to-point hubs like London Heathrow, New York JFK or Amsterdam.
So, if you want to know why Singapore Airlines or Cathay Pacific operates seemingly indirect Sydney-Singapore/Hong Kong-Johannesburg when it's much further to fly overall, the weirdly correct answer is:
they don't.
They operate separate Singapore/Hong Kong-Sydney-Singapore/Hong Kong and Singapore/Hong Kong-Johannesburg-Singapore/Hong Kong routes, but sell you a Sydney-Johannesburg ticket.