Nginx responds with 404 when the page requested is not found.
It is very unlikely that document roots of websites configured disappeared to cause missing files. However, it is worth checking if the original document root and files are still there.
If the document root of the website still there,
it is likely that a backend service responsible for processing pages for nginx is not running.
Example of such services includes apache, php-fpm, node etc.
It is of course very easy to happen such a case as many people will forget to configure services to start on boot.
So, it is likely that apache, php-fpm or node failed to stat after boot causing such an issue.
if that is the case, start such a service and configure that service to start on boot as below.
chkconfig service_name on
systemctl enable service_name