A rotary tool will not be good on wood that thick.
And with chipboard that thick cutting some fan holes in it shouldn't effect the strength too much.
You can use a large hole saw if you have one for nice round holes, I like octaganal holes for fans.
See here http://forums.hexus.net/project-logs...ml#post1920437
For cutting them in wood that thick, I'd drill a starting hole then use a jig saw to cut the hole, round holes should be fairly easy to cut with a jigsaw.