You might want to post this in the cases and cooling forum.
As someone else mentioned it is always about airflow. You have several sources in a case where energy is being converted into heat. That heat transfers to some other medium, air in this case, at a fixed rate. A given volume of air can absorb only so much heat in a given period of time, so you have to move the heat-laden air out, and replace it with air that is at a lower relative temperature so you can absorb some more heat. To make this process efficient engineers try to provide a lot of surface area where the hot thing can be in contact with air (heatsinks), and a lot of fresh cold air flowing across those surfaces. That's the whole cooling issue in a nutshell, and it doesn't really change with watercooling. All a w/c system does is effeciently transport the heat internally from the components where it is generated to a remote heatsink. They are more efficient in general because the fluid is a better transfer medium, and the remote heatsink is larger and more efficient than the one on the component in an aircooled scenario can possibly be. Regardless, the heat has to ultimately end up in the air, because all the heat on our planet is ultimately radiated to space.
So what happens when you take the side of the case off? If all you have are passive heatsinks in there, the cooling situation could actually get worse because you've disrupted the engineered airflow over the radiating surfaces. The temps on components with heatsink/fan combinations will probably drop, because those fans can now get more cold outside air to move across their radiators. But there may be other spots in the case that get a lot less airflow, where there aren't fans, or temperature sensors to alert you, that see much higher temps with the side panel off.