the only issues that I can think of are
1: extending all that fan wiring to under the desk.
2: access holes for all that wiring. Dont forget grommets so sharp edges wont cut thru the wiring.
3: drop in dc voltage levels due to length of wiring. I'm not thinking this would be a huge deal since you use a fan controller to lower the voltage to the fan anyways, just dont expect a full 12v or rpm's at the fan.