It's not really correct to say that Skynet stores all files 'by default in cleartext'. Skynet is a platform for building applications. Whether data is encrypted or cleartext is up to the app developer.

The files uploaded via https://siasky.net/ are cleartext, but the files uploaded via https://skysend.hns.siasky.net/ are encrypted. There are also entire dropbox-like apps that are encrypted by default, for example https://marstorage.hns.siasky.net/

Most Skynet usage is app-driven, and therefore whether or not things are "encrypted by default" will depend on the apps that are used.