Thanks for being honest with your feeling around in the dark approach and lack of intentionality in the design choices. It establishes that the design is flexible to optimization and that you are a pleasantly unstubborn individual 
Simple, effective approach to the fans- you are on the right track that you want to control them. Having them on all the time is a waste of power. However, what's the point of PWM/ controlling how fast it is they run?
If you treated them as simple on/off to cycle, and they were wired to a simple temperature probe (which is what you should be doing, as the purpose of the fans is to maintain temperature), they would turn on past a certain defined temperature, and turn off at a certain predefined temperature. That's the best approach, imo.
PWM/speed control leads me to believe the goal is "well, we don't need THAT much cooling just before our target temperature, so we'll run the fans just a bit". Sounds like a situation of equilibrium will be reached, perhaps the fan has to run at half speed 24/7 to maintain temperature. Wasteful.
From the noise isolation angle (which I think is completely unnecessary with these fans), treating the fans as full on/off, you can actually design your baffle and tune to the sound the fan makes at full speed. There's inherent compromises when you try to design a baffle that will work with every speed possible, because it will literally make infinitely varying frequencies of sound based on speeds. You can even assume that the designers of the fan have angled the blades in such a way that the optimal airflow to power drawn is at full speed.