When I see an issue like this in my modeling, my policy is always "take the path of least resistance". I try to find the tactic which will be cleanest, easiest to manipulate in the future, if I need to. If I were, for example, adding rivets to the side of a gun, I would use the method on the right, as it produces a much cleaner model. This is something which is much easier to undo, if I ever needed to. However, if I were to make the body of a car, I would want that to be all one piece. I will never be dissecting the body of the car once I have made it; it becomes its own physical object (for me).