Hmm... in theory you could run one magnet, but in practice what would happen is it would leave you with very weak spark. The magnets go around the outside North South North South, so as it sits on the end of a coil it pushes electrons from one side and pulls them from the other, as the flywheel turns it changes the poles and thus creates your AC output. But since it changes sines 4 times a rotation since it has 4 magnets, if you remove 2 of them on opposite sides then you will have a balanced but weak spark due to it not flipping as fast and only either pulling or pushing, not both; or you can remove two from one side so that the coil still flips but only once per revolution, and you better hope that it is at the same time the HT coil is charging otherwise it won't spark at all, while also being very out of balance.
My suggestion, if you don't care about lights then remove the whole damn flywheel, leave the points, and replace the coil that powers the points with a battery on the frame. use a 6V battery and run it. The points will still open and control the spark and you won't have any flywheel weight at all. Although you have to keep the battery charged, but if it's just for blasting and not daily riding who cares. Run the lights off the battery too if you want.