I left my 4" speaker ports open, for this very reason in the rear deck. But in all honesty, I have not seen the value of it that others have spoke often about. Maybe when I get my new dual 10's sub box created it will be different.
I am currently a running a 12" RF Punch in a sealed Sub Zero box so I am not blowing out tons of airs from the box. And my next box will also be sealed one, so I am thinking leaving my 4" speaker ports unused is kind of a waste. I might have to find some nice mid range 4" speakers to drop in there or something.