It doesn't matter what you do with them - burn 'em or plant 'em. They count towards a CV as soon as you get them (except through kidnapping, AFAIK).
I also think they count if they are settled in a city you flip or conquer. I know that you can collect Great Wonders this way, and they do count towards a CV. Which means, if you've built a GW in a border city, you risk not only losing it's direct benefit, you also risk losing the CV point and letting another civ get the CV point.
