"Banging" cookies half way through baking
Based on the recipe, it seems that the intended result here is for a denser, chewier cookie. If you were able to perform this percussive therapy maneuver in exactly the method desired by the recipe-writer, then yes, it would knock some of the air out of the cookie, and collapse its structure a bit. I think that this maneuver would be difficult to perform precisely and repeatedly. Also, you'll have lots of variation in cooking time, as you have to open the oven halfway-though which lets lots of the warm air escape from the oven.  

Instead of the "bang", just introduce less air into the cookies during the initial preparation. The easiest thing to do would be to under-cream the butter, peanut butter and sugar.