I removed the 6x9s in the rear, but I did keep the tweeters.
Basically it means I don't have much mid range in the back, but.. hey... I'm always in the drivers seat, so I might as well customize the sound for the front seats.
I've got tweeters and mids in the front doors, and I've also got dual action speakers in the dash. I've set everything up for quality, and not so much loudness. It just so happens it'* really loud... hehe.
I can basically crank my system up loud enough, with enough bass to pretty much rattle the car apart, and the speakers still don't crackle. Most of the time I keep the subs on 1/2 power.
I found that with the 6x9s removed, I left the stock grills in place, the subs "sound" better.