no it would not. if you want to throw a wiffle ball a tennis ball or even a cotton ball for the fun of it just do it. it will not damage your shoulder any more than any other repetitive throwing. repeated throwing of anything however could damage your shoulder over time if you are not careful and well-conditioned. you need to strengthen those shoulder muscles lift some light weights do some stretching/range of motion activities and get the proper rest between throwing. i am not sure what kind of ball you are throwing (i suspect a baseball) but stay on top of your game.
can throwing a ball that is too light damage your shoulder?