This is a more nuanced point but... they are always encrypted anywhere it matters.
1. On local network there's not too much point.
2. Over tailscale (or later iroh / holesail) the entire transport layer would be encrypted.
3. All comms about metadata is encrypted.
4. You can just drop encrypted files into the folder (e.g. nsync your cryptomater folder) and sync that - the protocol here wouldn't care.
