Sure, but the tried and true way to encrypt your NAS would probably be using full-disk-encryption, not something specific only to syncthing.
If you use Syncthing's encryption then at no point is the decrypted content available to the PI. It gets decrypted locally by other Syncthing peers after they have downloaded it.
[0] https://en.wikipedia.org/wiki/Wake-on-LAN
[1] https://askubuntu.com/questions/1269981/unattended-headless-...