Depends on the fan and location. I've got my 200mm fans running off molex to keep the air moving (and for the location/ needs its better), but they are bottom front and side, then my fast fans (high RPM) plugged into the MOBO so the system decides when they should run fast.
running them off molex will mean they run full speed all the time, there is nothing telling them to slow down. This means you will be generating more noise and using more power than perhaps necessary.
running them off molex will mean they run full speed all the time, there is nothing telling them to slow down. This means you will be generating more noise and using more power than perhaps necessary.