If Mega stores a file that is knows nothing about, that is fine.
However once that file is identified (and reported) as copyright protected, then Mega would have to take it down.
The point I guess is that Mega would be protected and the anonymous upload-er (if no IP was recorded) would be protected and eventually after who knows how many downloads, the copyright protector would be protected.
The down-loader would be protected if Mega doesn't keep track of IPs downloading any particular file, and there is no interception of data streams by IPS, the Govt., etc. identifying both the file and the IP of the downloader.
Yes the files could be encrypted, but somewhere there must be an index and a key and these must be distributed or the file is of no use.
Essentially the same as with data streaming using youtube as a kind of Mega.