From a noise suppression point of view, the exhaust pipe can be round, square or rectangular - it is the change in effective cross-section area (which causes a change in the acoustic impedance) that causes the sound to be reflected back 'up stream'. While the cross section shape of the pipe will affect the airflow, if nothing else the surface area would be different, I would imagine that it will not affect the airflow all that much.
A bigger challenge would be for the catalytic converter and/or DPF as changing the shape of these would be £££.