By taking those panels out you are susceptible to more dust buildup & noise. if you dont mind cleaning your system of dust more often & noise then its really a no biggie. Its one of those personal preference IMHO.
Sorry, I screwed up MODS: Can you please clean up my mess once again? ALSO, Why did it let ME pick the answer if I didnt pose it?
Actually this is incorrect. the fans are configured so that when the panels are in place, they channel the air over specific parts of the computer (CPU and graphics card)'. Having the panels off should not make much of a difference, however, with today's computers unless you plan on really driving your CPU. you should regularly dust out the inside weather the panels are on or off. My side panel is off for easy access, I run extra devices and do regular back-ups for people.