Taking South Africa in Global as Japan is a very, very niche play. It might make sense if Britain fell to Sea Lion, so that the South Africa factory is temporarily inactive – then you might want to seize it before Britain can build defenses there, with the idea of helping Italy turn into a monster and permanently keeping Egypt / Iraq / Persia.
But if you do Sea Lion, then typically Russia will be a monster and you will have trouble holding Romania and Poland as Germany, let alone the Middle East. Also, typically when Sea Lion is an option, Britain has done the Taranto raid against Italy, so Italy is not really strong enough to sweep through the Middle East even with no opposition from South Africa.
So really taking South Africa is a response to an Allied blunder – it’s handy if you can get it on the cheap, but it’s too far away and too strategically irrelevant to make a serious investment in it. It’s not a victory city, it’s rarely essential to taking or holding any other victory cities, it’s not worth a ton of cash, and it’s not immediately useful for securing a ton of cash. I think the main reason people like to threaten it is because they feel like a badass going so deep into British territory, but it’s not actually a reasonable strategy in 99% of games.