Why does shorting/putting heavy load on a motor slow it/stop it?
When a motor is free-wheeling it turns into a generator. 

By shorting out the motor you are applying a LARGE electrical load to the motor. If you want the generator to keep turning you need to apply a large torque.

Since all you have driving it is the inertia of the motor and whatever it was driving, this torque turns into a braking force.

You can think of this another way. Suppose you hook up a generator to a handle and wind the handle with nothing connected to the generator. The generator will turn quite easily. 

Now attach an electrical load to the generator. You will now find it is harder to turn the handle at the same speed. Note: YOU have to supply the power to run the load with your arm.

When you short out the generator, you are affectively applying a VERY LARGE LOAD. Turning it by hand becomes REALLY difficult.

You just built a brake.