Joburg and Cape Town are both Malaria free. You don't need malaria meds unless you're going up to Kruger or the extreme Northeast of the country.
ETA: I guess you could choose to take Malaria meds anyway but that would be kind of like taking them for a vacation to Florida so I'm not sure why you'd want to.
I'm kind of confused by the statement that they are optional. Wouldn't there be a malaria concern or not? If either area has malaria, I would take the pills. From another poster's response, it sounds like there isn't, so I wouldn't take them.
@32flavors Shit! That's crazy! We were there in July, so maybe that's how we were able to get a res. I wonder if your hotel has any pull?
We also really liked La Colombe, if you are looking for other ideas! Really, everything we ate was pretty damn good. The Biscuit Mill weekend market had all kinds of amazing food. We showed up there with full stomachs and didn't get to take advantage.