It controls them just fine. a 3 pin fan is voltage controlled, 1 pin for ground, 1 pin for voltage, usually 5-12v, and 1 that reports back the RPM of the fan, so the software just regulates how much voltage goes to the fans to control the speed.
A 4pin fan has the same 3 pins but instead gets a constant 12v voltage and the speed is controled from the 4th pin, a pulse modulation width signal, or PWM.
Which one is better? Meh. Both do the same job.