Systems to do this exist in the country (eg, moving water from Lesotho to the Vaaldam with the Highlands water scheme), but that project was 15+ years in the making, and is still ongoing.
From what I can see, nothing like this was realistically expected for Cape Town, and thus never planned for.
Not my area of expertise, but:
South Africa has some massive water transfer schemes: The Lesotho Highlands Water Project and others. The Western Cape Province and Cape Town are governed by the national opposition party (Democratic Alliance). It wouldn't surprise me if this led to a lack of coordination and plannning with the national government, if not outright neglect of the issue (along with general infrastructure-planning neglect between 1990-2005 or so).
It could also be profitable to ship out water inside grapes and, at the same time, import an equivalent amount of water in barrels. See it as Europe shipping water to SA to be packed inside grapes.
More likely, though, that is because Europeans are willing/able to pay more for that grapes/water. In a capitalistic world, it is the poor who will feel water shortages most.