RustDesk already encrypts connections going via Relay. Encryption is missing in direct IP to IP connections only - but you could set up an SSH tunnel, or a SOCKS or HTTPS proxy though.
Another valid alternative is Xpra, and it does support Wayland too - but doesn't reach feature parity with X11. Like RustDesk, Xpra is similarly feature-rich and mature, it too can take advantage of SSH tunnels, SOCKS or HTTPS proxies etc.
And then there's TeamViewer and AnyDesk - both of which are paid, with a free tier for evaluating or personal use - RustDesk is younger, but feature-wise they're quite similar.
Finally, you could set up wireguard that will happily encrypt your connection with very little overhead - regardless of your chosen remote desktop solution.
Another valid alternative is Xpra, and it does support Wayland too - but doesn't reach feature parity with X11. Like RustDesk, Xpra is similarly feature-rich and mature, it too can take advantage of SSH tunnels, SOCKS or HTTPS proxies etc.
And then there's TeamViewer and AnyDesk - both of which are paid, with a free tier for evaluating or personal use - RustDesk is younger, but feature-wise they're quite similar.
Finally, you could set up wireguard that will happily encrypt your connection with very little overhead - regardless of your chosen remote desktop solution.