You don't have to connect the radiator fans to the Ryujin's fan hub. You can connect them to a standard motherboard fan header. Check the fan ratings to be certain, but the 2 or 3 radiator fans should be well under 1A, so can be run from a single header on most motherboards. That should let you use the BIOS fan control, or possibly a Linux daemon (if there's a suitable one for your motherboard's fan controller).
Pump speed is a different thing, but you may be able to get away with just letting the Ryujin's default curve manage it. Water has a huge heat capacity, so you don't really need massive flow unless you are trying to do something more extreme.
I do wish ASUS would just publish the technical details for the USB control protocols, or provide some sort of SDK, but they don't seem to like doing that (same as pretty much all the other major brands, unfortunately). They make their money from the hardware sales, it just seems ridiculous to keep the software control so closed/secret.