Because desalination is expensive. It doesn't matter what the source of energy is, desalination interlinks water and electricity supply, much as corn ethanol interlinks food and fuel. And with estimated R15-billion capital outlay and R1.2-billion annual operating expenses for 164 million m3/year, as soon as the govt starts actually spending this kind of money, every lay person can think of better things to do with it. (Fix the leaks! Ban carwashes! Raise dam walls! End corruption!)

Anyway, on the merits, Australia is a better case study, and page 53 and 97 in the report below point out it's not all upside. That said, desalination in CT is inevitable over 10-20 year timescales. And so are dramatically higher water prices. But it's not some sort of missed opportunity. 

Unless you have Saudi-prince money, your garden will be dry with or without desalination. 

http://www.greencape.co.za/assets/Uploads/GreenCape-Water-MIR-2017-electronic-FINAL-v1.pdf