The part that's important is the server application and associated processes like the underlying Oracle database.
You can stop all of that with the cli command "ncs stop". Once that command has completed shutting down the application you can safely power off the server.
If you're adamant about shutting down the Linux OS gracefully as well, the switch to the root shell from the cli and do a normal Liunx "shutdown" command.
There is also the halt command at the ncs prompt. I'm not sure if that's available in the appliance or not. I suspect it is.