If ions are implanted in a silicon wafer as the term 'ion implantation' suggests, how can the wafer be electrically neutral after the semiconductor doping? Aren't the ions ions electrically charged? Or do we add/remove electrons from the wafer at the same time to keep the wafer neutral?
Yes, an electrical current neutralizes the wafer.
One uses ions in order to accelerate them to kinetic energies that will penetrate the wafer to a certain depth. The ions in this technique are positive. The wafer should not repel the ion beam, so it is kept at ground potential.