Yes, and also no. It really depends on your system setup. A properly ventilated case should perform as well as one with the side panel removed, some say better. I've heard that removing the panel results in small pockets of heat buildup. Without a thermal-imaging camera who knows for sure? I can only tell you what I've discovered about my own case. With the side panel off and only the PSU exhaust fan, CPU HSF and vidcard fan running my temps are 27/36C (system/CPU). If I replace the side cover these numbers jump 5C to 32/41C. When I switch the two 120mm fans (1 front intake, the other rear exhaust) on , the temps drop the same 5C. The noise is nearly identical either way. I prefer to have the side panel on. It looks better in my opinion and I can turn the two extra fans off to run near silent. Again, your results will vary. Every system is different and there is no magic trick capable of maximizing cooling for every type of PC out there. I feel that I've been very lucky with my setup. I'm running a full tower case filled almost to capacity with drives. The Celeron 1.3GHz I used isn't a speed monster, but it runs my apps just fine and doesn't double as a space heater. A great deal of effort was made to reduce the level of generated noise and many of the attempts failed. Keep trying and see what works (cooling, noise or otherwise) for you.
This really isn't the right place, but I'm on a rant so I'm going to post my answers on the two most frequently asked and easily answered questions on this forum:
q: What is the quietest heat sink?
a: All of them- heat sinks don't make a sound, fans do. So, what's the quietest fan? One thats not plugged in.
q: What HSF should I buy?
a: Depends on what you expect of it. A quality heat sink will disapate a large amount of heat ON IT"S OWN. The fan only serves to increase the airflow across the fins/pins to allow the sink to work more efficiently. Buy the very best heat sink you can afford and find the amount of airflow that brings your CPU temp to the range you find acceptable. Remember, system (case) temps will play a vital role here. One last point, dBa is a measure of sound. Pitch should also be considered when buying a fan. A 40dBa Delta screamer will sound very different that a 40dBa Panaflo.