Depends on the fan itself. So, model of the NZXT fan is?
Some 3-pin fans are quiet, while others are not. But when you connect it to MoBo fan header, you can often set custom fan profile for it. Or you can use fan controller and adjust the fan speed yourself, manually.
Also, do note that you can not get two at once: quiet operation and high airflow. It is always either: quiet operation and poor airflow OR loud operation and good airflow.
Yes, it cannot work with PWM control.
But, if your motherboard supports, you can work with voltage control on fan, instead of PWM. Almost same, sometimes even more precise (sometimes less precise though). But less efficient in terms of power consumption and heat (not that it will factor much anyways though)