I'll be the first to say 6.0's have a huge case of CANbus AIDS and do dumb shit that makes no sense, but the PWM fan speed logic in the ECU is based on directly measured coolant, oil, and ambient air temps with a side few modifiers based on whether or not the engine is idling or the vehicle is traveling fast enough to shut the fan off entirely (45mph).
I've been through a couple with no EGR, but EGR was set to not present in the ECU. I'm not seeing how EGR removal would cause this - was it replicated on multiple trucks, or was it just one truck that might have had a wiring problem? If I saw one doing that I'd wonder if it was a bad fan clutch or headgasket; deducing the lack of an EGR valve as causing it would be a diagnostic fuck in the ass.