Hi!
I have the same problem on a Gigabyte X570S AORUS Elite AX mainboard. The pump connector (3-pin) from my Be!Quiet Silent Loop 2 is connected to the header SYS_FAN4_PUMP. However, AIDA64 Extreme only reports the speeds of the PWM fan hub connected to the CPU_OPT header.
The pump speed is read out by both the UEFI and by Gigabyte's "bloatware".
Strangely, AIDA64 also reports fan speeds for "GPU" & "GPU2" although there is only 1 graphics card installed (Gigabyte GV-N3080GAMING OC-12GD with the Windforce 3 cooler). They appear to be the same, based on the reported speeds.
KR,
Kevlar