The orientation of the Master and Slave on the cable will make a difference only if you are using Cable Select (CSEL or CS) to determine the priority of the drives. This is because pin 28 is grounded on the Master connector (Drive 0) and open or not connected on the Slave (Drive 1).
If you are using older components not all cables, motherboards and drives may recognize Cable Select. All of these components must recognize Cable Select for it to work successfully.
Do not attempt to use Cable Select with any cable unless it has three differerent colored connectors. The blue end connector attaches to the system board or host controller, the grey middle connector goes to the Slave, and the black end connector goes to the Master drive.
If you are using the Master and Slave jumpers to set the drive priority then the cableing sequence will not be important.