Yes, you can see the numbers on the finished product, but without them you wouldn't know where to glue what piece, and you'd just end up with a lot of rainbow coloured paper waste
Would it be possible to upload a version without numbers? Or have the numbers printed on the tabs and next to the matching edge? That way you wouldn't have any numbers showing on the final project. Same for the Applejack hat. If you'd like an example, Darth Biomech does his papercraft ponies like this:
darth-biomech.deviantart.com/g…
darth-biomech.deviantart.com/g…