Definitely following the same route; Middle east via WACS would be a whole lot higher. Issue here is purely geography - the middle east route for AWS runs out of Mtunzini in KZN. There is no direct path between CPT and DBN (yet, there are two coming online next year). This means from CPT, traffic needs to go to JHB (+- 20ms) then on to KZN (+-9ms). Not sure where the rest of your latency penalty comes from (probably some processing overhead). But if you were to trace to the server, you'll definitely see a 20ms penalty on the CPT-JHB leg.
With regards to the new Trenched CPT-DBN and submarine (Africa-2) routes, no official figures are out regarding latency, but we're hoping to see some improvements on East coast routing for CPT users once adoption on these cables goes up.