Like any other form of third-partyupscaling, third-party Waifu2X upscales are only accepted if the original version is not available, and should be flagged/deleted if the original picture is uploaded.
If you want to upload a picture that has gone through Waifu2X, follow help:image source for instructions on how to try and find the original picture first, and only upload the upscaled version if reverse searching fails.