Is it bad to run a PC that has holes in the case?

I have an Enermax case with the Enermax logo carved in the side panel w/ Plexiglass behind the cutouts. I took the Plexiglass off so I could get better cooling and it helps. I was wondering if there are any disadvantages to it regarding electromagnetic interference. When I was studying for A+ certification I read the case has something to do with reducing elec. interference so just wondering if anyone else does this and had any problems.

It will let the dust in...and if enough dust accumalates then ESD can happen...but if you keep your system cleaned out, then you really shouldn't worry that much...unless you live in a dusty area like I do...even with the case sealed I still have to clean it out every few days...