Even if the data can be secured from being read, there is proof that one computer talked to another computer about something. That's often enough "evidence".

Tor/i2p mostly solve that problem.

Frankly I don't see how the internet can be secure. AFAIK, it never was.

"internet" is not secure, but you can build secure communications over insecure transports as long as you are able to do initial key-exchange somehow securely (ie. face-to-face meeting). Something like OTR with Tor hidden services is very secure.