A six CD changer...? Are you sure? The V6s came with a 10 CD changer as far as I was aware - mine has a 10 CD changer, tucked into the side cupboard on the lefthand side of the boot.
If you have an ipod/MP3 lead hooked up to the back of your car stereo, you'll be setting the stereo to the CDC (CD Changer) setting to use it, which means the CD changer isn't connected anyway.
No harm in taking it out, I couldn't tell you if it's worth anything though. Perhaps ask on the forums if anybody is looking for one, if there's a buyer out there, I would expect them to be on this forum!