I can't imagine getting my full doors into the back of a TJ without throwing out my lower back and being bedridden for 5 days, not to mention having them loose back there is bound to damage them from banging into one another, or kill me in the event of an accident.
For half doors, I could see if they were well constrained to not crash around back there, but the open air feeling is plenty present enough to feel no compulsion to remove them.
If you're talking about soft upper doors that slide into half doors, then yes I do it all the time because my wheeling spots are hours away and I like to wheel without them but don't want to get beat up by the wind the entire way there. I have a bestop bag for them to keep the vinyl from getting all scratched up.