Johannesburg is ranked 18th in the world with regard to high altitude cities and can only imagine the health problems living at a higher altitude. Yes your body does acclimatize and adapt over time so it would depend on the individual.
Johannesburg is situated 1753 m (5800ft) above sea level and is the highest major city in South Africa. The air is much thinner than the coast and takes an extra minute to boil an egg in comparison to sea level. Apparently endurance athletes do come to Johannesburg to train as the advantages of training at altitude and heading to lower levels for an event is beneficial in how your blood stores oxygen. One side effect is your blood does thicken and I guess that is not the best for someone like myself who has suffered from blood clots in the past.
Recently we had to go to Durban for a business trip and even though the time spent at the coast was only 3 days the difference was very noticeable. The sinuses tend to open up and clear very quickly compared to being bunged up in Johannesburg. Your ears pop on the way down to the coast due to the change in pressure and pop again on the drive back up.
When I arrived in Johannesburg back in 2008 I never had any sinus issues and these days you forget as it feels like you are suffering from permanent hay fever. Taking a break at sea level on a regular basis is then seen as a must do exercise which you don't realize the benefits until you have done this.
I mentioned in a post yesterday that the mine dumps do also create a problem normally during the months of October and November when Johannesburg has the windy months before rainy season kicks in. The dust can be confused with pollution which is like a browny type layer one can spot at sunrise and sunset. This is probably a mixture of both dust and pollution which you cannot miss at certain times of the year. Obviously this is not great for ones health as who knows what you are breathing in.
The altitude is a real thing that does affect your breathing as oxygen levels are that much lower. In the past sporting teams used to arrive a week before an event to help acclimatize themselves and the trend these days is to stay at the coast and fly in on the day of the event and fly out immediately afterwards. The players will run out of energy that much faster and will not be able to perform at the same levels they would playing at the coast. This is why when planning a tour local organizers will arrange game son the highveld between games at the coast so this handicaps touring teams and is like a home advantage.
The long term plan was never to stay in Johannesburg and that is still not the plan as knowing this impacts your body on so many levels like with affected sleep and breathing this is always in the back of your mind. Living at the coast is that much more pleasant which is the ultimate aim at some point in the future more so for the health benefits and quality of living.