A shunt doesn't protect anything, it just lets you measure the current.
If it's a fuse, then yes, that can help protect the motor if the controller failed shorted, and probably the batteries if the controller shorts, but it might not blow fast enough to protect the controller if something failed at the motor and drew so much current that it needed to pop the fuse.
Can your controller take 100A continuous for at least 30 seconds? Can your batteries take that? If not, you might want a smaller fuse.
You want one sized to blow a bit before whatever it is protecting would blow, or at whatever you consider the maximum limits of the system's weakest part.
As for a kill switch, as long as it is a switch that totally cuts off power from the batteries, that's probably the safest, as it will stop the largest number of possible failures from causing a fire, etc.
If all you want it to do is stop the motor from running, then anything that turns off the controller (assuming brushless) will do that. Even an ebrake line will do it.
If it is a brushed motor/controller, then the only good way to stop a runaway motor is to cut the battery power. Because of this, CrazyBike2 actually has several killswitches:
1: Run-stop-run switch on handlebars. This is in series with the throttle, and disconnecting the throttle disables my controller.
2: keyswitch in handlebar stem. This connects to a keyswitch input on the controller to turn it on and off. (used to just be in series with throttle, too, on the 2QD).
3: Toggle type circuit breaker next to my left knee. This is in series with battery negative, and will cut power to the whole bike.
4: Andersons on batteries next to right knee. Pulling any one of these out by yanking a wire and pulling will disconnect at least one battery from the series string and kill all power.
You don't need that kind of insurance with a brushless controller, though.
