I don't think it went to CPT, but to JNB. None of the VC10 variants quite had sufficient range to do LON-CPT (6011 miles) or JNB (5636) nonstop with a viable payload.
The reason for the NBO stop was most likely that, as well as refuelling, they could carry revenue traffic on both segments (LON<>NBO and NBO<>JNB). I think some services went via Lagos, Accra, or Kano.