ghost install and ghost setup automatically ask if we want ssl after the nginx stage. Not sure if doing just ghost setup nginx also asks or not. In any case, the optional ssl stage requires a previous nginx stage.
As Vikas suggested, and I agree, it’s a good practice to have an Nginx file or symlink for each domain in the sites-enabled folder. Anyway, probably you have this line in your /etc//nginx/nginx.conf file:
include /etc/nginx/sites-enabled/*;
So I guess it’s possible to merge files, although I’ve not tried that. It’s more ordered and it’s working well as they said you.