I don't know how the build in noise reduction affects RAW files but it is irreversible if it does. I always have every camera noise reduction turned off because I like to control as much as possible manually. I assume that an actual version of Canon DPP does a better job in noise reduction than the image processor of your camera but I haven't tested it yet.
Unfortunately, Canon DPP offers you only a choice between lesser noise or details thus I stopped using it after finding a better program for noise reduction. If you would like to get more detailed photos, I suggest you to do the same. I know you wouldn't like to hear that but I get much sharper and more detailed results with the noise reduction of NeatImage than with Canon DPP when processing the 16-Bit tiff file. As you can see here
(click download for larger resolution), I get very sharp and detailed results when using ISO 1600 with my EOS 400D by reducing the noise with NeatImage.