First, what do you mean by "let?" Do you mean you mean you just assume that the puppy will occasionally have an accident, and the pads are there to contain the mess? Or that peeing/pooping in the xpen is going to be standard practice?
To my mind you should start as you mean to continue. I personally do not use pee pads in the xpen. First, I don't use them for adult dogs. Therefore, I don't want to habituate the puppy to peeing on soft surfaces. Second, I don't want my dog peeing indoors, period. I don't want the dog peeing in the xpen, the kitchen, or any place else where he can look up and see ceiling. That means taking the pup outside frequently and crating him when I can't watch him. Finally, puppies have a tendency to turn pee pads, bedding, and everything else in their xpen into toys. I would rather not have to clean up shredded bits of pee pad.
Of course, I have a yard, an uncarpeted room where I can put the xpen, and a spoo. I might feel differently if I had a small dog in an apartment on the 19th floor.