Freenet was never really anonymous; there have definitely been busts from Freenet. IIRC it’s distributed, but not anonymized; I haven’t really done anything with it in ten years or so. i2p is probably pretty solid, but it’s often very difficult to use. I’ve tried it, and most of the time couldn’t make configurations work. Or else the eep sites I was trying to reach were offline. IDK.
I dunno; given that Tor was originally designed to be extremely difficult to track, and was designed by spooks, it’s plausible that they aren’t able to crack their own security. If they controlled enough of the network, they could, in theory, track individual users. But it would be extremely resource intensive, and they would already have to be targeting you.
IIRC, the case you’re talking about involved social engineering to gain admin privileges, then illegally hacking computers through malicious javascript to leak their real IP. IIRC a huge number of the cases ended up getting thrown out because there was no way they could legally do what they did, and the convictions they did get were ones that they would have been able to get without the illegal hacking. That was, what, something like ten years ago? Around the time that The Silk Road got taken down? (That was taken down because the site owner used the same username both on the Silk Road and on a clearnet site; he essentially doxxed himself.)