Not that I agree with this, but the area the holes would be drilled is below the filter so the air still would be filtered, but the filter would need to be changed more often, and this mod would increase the chance of more water to be sucked in if the box gets under water.
2004 GC Spec. Edit. V8 4x4 Quadra-Trac II. Bright Silver Metallic Clear Coat, 4" lift, RE shocks, adj. JKS CAs all around, 265/75/16, 10 ply., Maxxis Bighorns, ProtoFab winch bumper, Vortex 10,000 lb. winch, dual OME steering stabilizer, Rockyroad rockrails, skids, JKS Discos. Addco front & rear sway bar, & Aussie locker. Next year? : Rear bumper with tire carrier.