The only issue I see with vending it out the side is the position that the smoker will have to be in. I plan on have the back facing the wall... not the side.
I have a cap on the end of my exhaust now that I use and I have no issues with the wind. If I did it through the roof, I would have something similar on that exhaust as well. I would also cover the vent while the trailer is not in use.
This is the cap I currently use