I disagree with your comparison to criminals. Gathering evidence for a case can be done at any place relevant to a case. It is sad to see that they confiscated materials owned by a witness, but within the bounds of "reason": they are a related party in said case.
Please note: I do still, from what I read here, find this excessive use of power. A normal warrant with a request for data could very well have been enough, but that's guessing what kind of evidence the police expected to find.
The police took way more than they were allowed to by the warrant they got, a warrant that was already completely illegal. This is absolutely an overreach, the police, the staatsanwalt and the judge involved are standing outside the law.
They obviously wanted data from Riseup, about some email address. Which I gather has no presence in Germany. So they went after Zwiebelfreunde.
That seems ridiculous. I mean, there's no way that Zwiebelfreunde would have any data about Riseup's email accounts. Even Riseup claims to retain nothing.
I suppose that Zwiebelfreunde might have handled contributions to Riseup from someone using the targeted email address. So there might be a money trail. But that's pretty iffy.
Witnesses can be raided under german law, there are some reasons for it, esp. when it's suspected the witness is hiding evidence.
However, the raid is still out of bounds in certain other aspects (though I suspect the "take everything" the police pulled is more related to the officers having no idea what a server is vs a desktop computer. It wouldn't be the first time police officers simply don't know so they take it all)
Search and seizure does seem like a bizarre way of being a 'witness'. I suppose this is a response to Zwiebelfreunde being expected to not reveal the information they seek.
Wow, so the witnesses are treated like criminals now.