Yes, you can cut nice neat holes, or you can just cut the entire bottom out, whatever you want. The idea is to get air in thru the bottom of the box instead of sucking it in thru the saxophone snorkel.
The benefit is there is less restriction, so you suck in slightly more air. The detriment is that air is warmer, so it is less dense. People have reported better results by yanking the snorkel out of the fender, instead of cutting up the intake. On the other hand, the cut intake sounds better.