The overclock on the EVGA Superclock is relatively small at 726mhz vs. 700mhz on stock. That much of an increase does not cause any additional heat or result in higher fan speeds. That particular card also implements a customized backplate that is supposed to improve cooling and airflow. Additionally, the cooler exhausts heat outside the case, so it shouldn't cause any problems overall for your other system components.
In my testing on an Asus GTX480, the temps and fan speed only really start to increase when pushed above the 760mhz level, but then only by 1c or 2c with the fan up to ~78%. However, with these cards, let alone two in SLI, there really is just no need to overclock at all, and particularly not to the point where noise and heat become a concern. I keep mine steady at 726mhz and Auto fan, just for fun.