I can vouch for how noisy they are, and as you say the PWM way is the correct one if you are going to use a fan.
The Pi itself seems reasonably comfortable to run hot. I run hifiberry metal cases which are pre drilled for a fan and I want control of it without going to the tedium of adding a switch.
Drive from the 5V. the 3.3v line doesn’t need that fan noise, but to do so you will need a transistor to operate the fan.
Here it is from the original thread…