I don’t think the original MegaUpload site hosted encrypted files, at least not in a zero-knowledge way. They also encouraged users to do things like upload their entire music libraries and had a searchable database of them called Megabox. They weren’t just a file hosting provider, they were in many instances encouraging their users to upload pirated content and had all of the tools to see what was being uploaded and what was infringing.
It’s only a matter of time. If they don’t release it, someone else will release something comparable.