A very small flywheel won't do much if anything. A large one would need to be very carefully balanced not to make things worse. The faster a flywheel spins, the more critical it becomes to balance it, and the better the bearings would need to be. Most CNC router spindles go at upwards of 18,000 RPMs. While it's possible to run pulleys off a flywheel and spin them slower than the tool, that introduces a lot of mechanical complication. Also the weight of a flywheel would increase inertia, and make it harder for the machine to change direction. I think these reasons may have something to do with why you never see flywheels on machines like this. If you're noticing chatter in your cuts, increasing the rigidity of your machine would be a more promising remedy.