With the newer magnets out these days, zapping the magnets won't do much unless you have a custom made high powered zapper. Think of the magnets as a glass of water... you can only fill it so full. Magnets are getting so good, that they are fully zapped when you get them.
The main advantage to zapping the magnets now is to center the magnetic field. Motors don't always come zapped perfect or 100% centered from the factory, so zapping them at that point may help. To test this, take your gauss meter and check the magnet in multiple spots. If the reading is the same, you have good magnets. If you get different readings, then it isn't centered perfectly.
If you heat up a motor a little, it shouldn't hurt the magnets much if at all. If you REALLY cook the motor though, it does hurt the magnets, but it also hurts the comm for life, even if you cut it. The extreme heat changes the hardness of the copper. This difference may not be night and day, but it can be noticable. Hopefully this will give you an idea of what is going on with the magnets inside those little powerhouses