Ever since I set up my first VPS to use nginx two years ago, I set it up the way everyone said to with two directories: sites-enabled and site-available with symlinks from available to enabled. This is usually cited as the "debian" way or style.
But by default, debian's nginx.conf includes conf.d/*.conf. It seems to me that the Debian way should be to simply put domain.conf into conf.d, and if you want to disable it just rename it to something like domain.inactive or domain.disable.
Am I missing something important? To me, this seems far simpler than dealing with two directories and symlinks.