VNC Server Unencrypted Communication Detection on Mac Mini's

In order to have a VNC encrypted connection, an SSH tunneling is required (as described in the links you provided). In my case I usually type this command in client's terminal:

ssh -C -L 8000:127.0.0.1:5900 username@your-external-IP-address

Where username and your-external-IP-address (or domain if you have one) are the ones belonging to the machine you're trying to connect to.

While keeping the terminal open and running, a VNC sessions is then started with vnc://127.0.0.1:8000 in Finder -> Go -> Connect to Server...

Another option is to set a VPN and connect via VNC through a local IP.

Regardless of the solution chosen, your internal security scan will still report that a potential unencrypted VNC communication is available because the machine will still "listen" for a plain VNC connection.

If you start a VNC session (or any other protocol like AFP, SMB...) tunneled through SSH, then it will be encrypted.

As said an alternative is to implement a VPN.

Otherwise there're apps like Remotix or Screens which simplify the process (no terminal involved) or web services like LogMeIn.

I don't know why you get the "VNC Server Unencrypted Communication Detection" alert.