erm.. i dont think so tbh.. I think the reason is much more practical..

Dust.. when the Heatsink would fase upwards, it would catch a lot more dust,.. not to mention that it is much easyer for BIG pluche pieces to be sucked into the fan and block the air to flow through the heatsink completely. sjeesh... you guy's really need to learn something about cleaning stuff..
Edit: also... if a cable (a 4pin molex for example) hang's loose... when do you think its more likely it gets stuck in the Fan of the grafic's card's cooler... when its facing upwards or downwards?