"The duplicate files under the modules/pages folder should not have an impact on the performance of the site. However, they're quite a few files there and it can make things a little cluttered. I'll probably look at addressing this in a future release."

Look at the way jquery lightbox is working now, it uses javascript loader to load js on pages set in admin. The point is to be able to enable lightbox on any page without having to do anything with the js and css files.