The site is shut down so the people involved have achieved their goal. I doubt that the defence is claiming that there was no copyrighted material in the users

The site is shut down so the people involved have achieved their goal. I doubt that the defence is claiming that there was no copyrighted material in the users data stores. The case is really about refusal to pursue copyright enforcement. All the prosecution needs to do is drag this out to win. So if you don't toe the line all your equipment gets seized. If you ever get it back it will be obsolete. You will also be tied up with legal stuff for a long time. That is the real message being sent here. The facts of the case don't matter.