It might, and it might not be. 3-pin fans can be controlled with no PWM using the older method of voltage regulation via the motherboard or hardware resistors. The latter come with enthusiast fans, ones like from Noctua, where they implement cables with resistors in them to cut the voltage of the fan from 12v to 7v or 5v.
Motherboards used to, and still can in most cases, control fans in this same way, but are able to vary the speeds just like PWM. The deal is, PWM is less harsh on the fan, makes for a wider range of control of the speed, and is more efficient.
The easiest ways to test this is:
1 - Check your BIOS configuration for fan speed settings. Usually in the Hardware Monitoring section.
2 - Run something to stress the CPU and see if the fans speed up any. Things like Prime95 or IntelBurnTest. AMD Overdrive also has a stress section.
If the fans are being controlled by the motherboard, they should not be able to be controlled by speed fan. Good luck!