Apache goes against the Debian policy on this one. They have to because of some hacks in some plugins that are supposed to enhance security. The default is simply a default. Some people will actually store websites in /etc/nginx/www/ on debian systems. There's no way to correct everyone that isn't willing to learn how to administer a system.
Even if we stick things where they don't belong (/var/www/html), people will still treat that like what they should overwrite which means we would then have to manage the package maintained version and the user version.
I'm okay with sticking a README file in the default location, but ... I really doubt anyone that needs to read it will actually read it.
For reference, I'm maintaining the package, and the first thing I do after installing nginx is rm /etc/nginx/sites-available/default. Some people prefer stuff be in /var/www, some prefer /srv, some even think /opt, and yet others think everything should be in /home. We adhere to the Debian policy which leaves the admin free to do whatever they want by way of simply creating their own config instead of using default.
Honestly, my intention with the default config was "it works", here are some examples and a quick intro to a config, now do it yourself.