If cable assemblies are so great, why use wire harnesses? One possibility is that some cable requirements are not very extensive. It's just easier and potentially more economical to reserve wires, creating a cable assembly as needed, rather than stocking up several coils of multi-conductor cables. Another time when it’s really important to use a wiring harness is when you have many branches coming from one connector in a cable. A good example of this is a PC power cable harness; one end is connected to the PC power supply, and it has many branches connected to the hard drive, motherboard, leds, etc. Cable assemblies are not suitable things to use here because of all the branches.
If you have a requirement with many branches AND some controlled impedance such as in RF cables, you can include cables within a wiring harness to achieve this. Often the terms wiring harness and cable harness are used interchangeably.