Adding more ports is a way of getting more port surface area without having such large ports that the piston gets stuck in them.

For example if you make the exaust port super wide, the edge of the piston can catch on it. So you make three exaust ports, one large in the center and two small ones on either side. This effectively make a much larger port to evacuate the exaust.

Intake ports are a little more complex. You are still increasing port area, but also controlling the flow rate and direction around the piston and into the chamber to increase swirl and reduce air/fuel from being thrown out the exaust port(s).

Now you take a stock 3 port and have it modified by a tuner(Rody, Colari, etc), they maximise port flow, direction, intake and exaust timing, even releave the inside of the case to obtain much of the same effects of having more ports.

This accounts for how a modified 3 port can out perform a 5 or even 7 port motor.