I don't think they could have known for sure it was a joke.

The judge’s point is that if they want to sue anyone for misleading them, it should be whoever sent them the message. He’s not saying they would necessarily win that hypothetical case.

So why shouldn't Snapchat (who presumably reported it to the government) be charged for the same offense of reporting a non-threat?

I'm not suggesting they should be, but just following the same logic as your comment.