How will I know if it's whining before I buy it?
No way to know, its the luck of the draw, personally i think its a combination of hardware, not all have this issue, for example i own two seasonic x series (660 and 400) both been perfect.
I don't have much choice around here with the boards. The Intel one is more or less the only Q87 board I can buy.
Dont worry the intel should be fine, i also did my HTPC on a Q67 board and all work out fine, and if the cheapest you can get and available, you should be fine with it. Although check if they have B85 or H87 versions of the intel mobos as they should be cheaper... but you never know.
There's also a SuperMicro model available with that chipset, but costs twice as much.
I built my server on Supermicro motherboard, and its a great motherboard but has a ton of things that might not be worth it to you, so i would stick with the intel as its cheaper.
As far as I understand PWM reads data from mobo temperature sensors. So how can that be helpful if I wan't to cool down the hard drive. Let's say hard drive tmeperature is fine at lowest fan R.P.M. If the spot on mobo, where sensor is located gets warmer it will raise the R.P.M. and make unnecessary noise, because the hard drive doesn't need more cooling.
Well in reality there is no motherboard that i know that could use the the temp on hdds no matter if its PWM or not, the boards come with mulitple sensors on them (CPU, Sys temp, etc), on most intel motherboards the CPU temp is what drives the PWM signal, as it is in most (not all). Personally i dont think you should worry about hdd temps, most of the green hdds will not even need direct cooling, i have had most of my hdds on my pc without a fan and been fine for years, even if its a low rpm it should be fine. I be more worried about maintaining the CPU temps under control, thus about the airflow on the case.
Now i think your idea of the Noiseblocker M12 S1 is great, and should work fine. But if down the road you want to try PWM fans, the intel mobo should be fine also, just its important to chose fans that can drop low on pwm signal, if you do consider Noctua NF-S12A PWM
and a cheaper good alternative Scythe Glide Stream SY1225HB12M-P (300-1300rpm)
As for cooling CPU's PWM can be handy, but I fell I can't get enough control over it in my current system. I use stock CPU cooler. PWM in BIOS is set to the lowest setting, and the fan never spins slower than 1300RPM, eventhough CPU temperatures mostly sit around 45°C never rise above 50°C, which is still 15°C lower than max. allowed temperature.
Remember the PWM signal is just a signal that we interpret as a load in %, so it will depend on the design of the fan, for example the intel cooler uses an 60mm fan (or 80 not sure), but due to the size and that intel standardizes their coolers, they design it so it doesn't go much lower than 1300rpm, but other fans are design differently like the ones above, they can be drop down below 400rpm on pure bios (as long as the motherboard allows it, intel in my experience does). Here is the fan curve for Noctua NF-S12A PWM on Asus motherboard with FanXpert2 on a true PWM fan header (CPU_FAN),
Just for your reference, i also tested recently one of my Noiseblocker M12-S1 on the Asus motherboard with FanXpert2 on a fake 4pin (voltage controlled CHA_FAN3) header, here is the graph in case its useful to you,
At the end is a matter of preference, 3pin is fine and 4pin PWM is also fine, personally i just prefer PWM as i can plan my setup to dynamically ramp up without any software depending on the conditions of my CPU. Usually all my fans case fans on all my builds are at 300rpm or lower, and once the temps of the cpu rises the rpms rises, and if the cpu temp lowers the fans rpms lowers as well.