Any reason for them to be turned on by default if they dont do anything?
Maybe partly because that's how the Arduino is set up. All of its timers are up and running. I am in favour of this because setting up the hardware is often one of the biggest hurdels for a beginner to overcome.
I imagine it also makes some of the other code, like pwmWrite, a bit simpler if it can assume the timer is already going.
Finally, the timers are doing something, they are running!-)
So it is pretty straightforward to go look at a running timer to get a value. IMHO, this is very beginner friendly, and makes 'foraging' around the peripherals easier to get started on.