If you do it right, it shouldn't cause significant wear to the punched cards. You'd want to move the cards with the pins up, and then drop the pins (read head) after moving them. Each pin wouldn't need to exert much force on the paper, nor should the pins be dragged in and out of the paper hole. From everything I've read, the card sets were used many times -- at least one mention on the wikipedia article of a set of cards being used over 100 times.

Oh, and wikipedia has a nice figure from, I believe, Jacquard's patent.

https://en.wikipedia.org/wiki/Jacquard_machine#/media/File:T...