The Why? part mainly is my being cautious because the Kraken manual does NOT tell us exactly how it does some things, AND the mobo manual does not tell us all the things SmartFan does.
This could get complicated in details. SmartFan is the system built into the mobo BIOS (probably not a software utility loaded to run under Windows) that manipulates fan speeds to keep temperatures on target as measured at specific sensors. It also MAY be involved in actually counting the pulses in the fan speed signal lines to display fan speeds, although that function is not needed for fan control. So if you turn SmartFan off, I am not sure whether the BIOS will do the fan speed reading job. An important second function of the CPU_FAN header is to monitor the speed of its fan (in your case, of the Kraken PUMP) for FAILURE and generate a quick alarm and protective action. I expect this would be done whether or not SmartFan is Enabled, but I don't know. Now, CAM can tell you the Rad fan speeds AND the PUMP speed of its system. For sure the rad fan speeds it gets by a counter device built into the pump, which is where you plug in the rad fans. SOME such systems actually get the PUMP speed from the mobo CPU_FAN header since you plug a cable from the pump into that mobo header specifically to sent the pump's speed there for failure monitoring. But it is also possible that, just like the rad fan speeds, the Kraken system simply does its own pump speed measurement rather then get it from the mobo CPU_FAN header, and communicates that back to CAM via its USB data cable. The problem I saw is that we do not know exactly how the PUMP speed is being monitored, and whether that requires SmartFan to be Enabled.
Regarding CONTROL of the pump speed, we can get some info from the fact that the cable from it to the CPU_FAN header is a 3-pin type. Because of the differences in design between 3- and 4-pin fans, when a mobo fan header is set to use PWM Mode, it can NOT alter the speed of its fan, and the fan always runs full speed. So SOME AIO systems use this as the way to power their pump that they WANT to run full speed all the time. However, the Kraken X63 system provides all power for its Pump AND fans via a direct cable connection to a PSU SATA power output, and does NOT need ANY power for the pump from the CPU_FAN header. Fot this reason I suspect that the "cable" from the pump to the CPU_FAN header actually has only ONE wire that connects through Pin #3 (the speed line), and the Kraken system uses its own means to power and control its pump. HOWEVER, the manual does NOT say this clearly, so we are left to guess. So as a precaution I advised leave SmartFan Enabled, and set the CPU_FAN header to use PWM Mode.