This command only deletes the certificate.
If you want to remove a domain from using SSL, you should disable the file it runs SSL in: unlink /etc/nginx/sites-enabled/<file-name>.conf
[presuming the file only has the one domain in it - if not, you may have to remove the part(s) manually]
[the actual file should still remain in the /sites-available/ folder (unharmed) for possible future use or review]
[don't forget to restart/reload nginx]