Nginx: Redirect both http and https root to subdirectory

This configuration will do what you want:

server {
    listen 80;
    server_name example.com;

    return 301 https://$server_name/subdirectory;
}

server {
    listen 443;
    server_name example.com;

    location = / {
        return 301 https://$server_name/subdirectory;
    }
}

The = / specifiers means a full match, so it matches only the exact root URI of the virtual server.