Luke
On a few Malibus, we have lengthened the pass thru hole for the ballast hose and steering cable for exactly what you are trying to do. It was necessary to push them back a little in order to gain a little but much needed enclosure depth. So, take a light and look into the hole. Feel around as well. As long as the direction you plan to cut is into the bilge, then there should not be any issue.
As far as the box goes, with any sub enclosure, getting the internal volume correct is key. With a ported enclosure, shape of the box and port design and volume is next on the list of importance. You will not have quite the flexibility with the shape of your ported enclosure as you would if you were doing sealed enclosure. So notching the box around cables may be doable, but could end up effecting the port design and its exit point, thus complicating the build. I would look at moving the cables first then adjusting the LxHxW to accommodate the cables while trying to keep the net volume the same. Keep in mind though, adjusting those dimension will change the ports opening and length. This will change the tuning frequency, so those port dimensions will also need to be adjusted.
Michael
Mikes Liquid Audio