Fortunately, our bags made it safe and sound all the way to Cape Town. We were a bit worried as it took a while to spot them on the carousel, but they were there. We actually ended up with 15 or so minutes to spare, but that's because we practically ran to the gate. It's a big airport and our gate was fairly close (considering the size of the airport). Had we been any farther or been delayed any longer, I doubt we would have made that flight.
OP, if you choose to go through Amsterdam, I'd recommend about 2 hours in between flights in case of delays. We had an hour and a half, which is clearly doable, but two hours would have been less stressful. Of course, with no delays, 1.5 hours is plenty, but I've heard delays to/from this particular airport are frequent.
We also arrived 2 days early to explore on our own, something I highly recommend. It gave us a chance to adjust and do some things not included on the tour.