if the area ur removing has some sound dampening on it, sure, but the fans already being quite should minimize that. Then again it's usally ur CPU fan that makes most noise.
well I have a clear xoxide case, so from my case noise, which is sugnificant(15-fans) and stock AMD fan on 5600 64x2 athlon(noisest item), the clear window will increase your sound lvl. but if the noise is not too high pitched it should be minimal, casue if it wasn't for my cpu fan whining, i would be very impressed w my fan noise.
I would say larger slower fans are the way to go for low noise lvl. i'm tinking of upgrading my cpu fan just for the noise lvl, nothing to do w cooling temp for my concern, because using the asus fan controlls is fine but then u end up with up and down cycling and that's almost as anoining as being loud.
hope this helps, go for it, it should be tollerable.