The debian/dirs only makes sense while building from debian source package, in actual debian package
it has no significance (You can confirm it by looking inside control.tar.gz of nginx-common package).
You can include empty directories in a deb without any extra effort/flags
$ mkdir -p foo/{bar,zero}
Created deb package {:path=>"foo_1.0_amd64.deb"}
$ fpm -s dir -t deb -n foo -v 1.0 foo/
$ dpkg --contents foo_1.0_amd64.deb
drwx------ 0/0 0 2013-07-30 15:40 ./
drwxr-xr-x 0/0 0 2013-07-30 15:40 ./foo/
drwxr-xr-x 0/0 0 2013-07-30 15:34 ./foo/zero/
drwxr-xr-x 0/0 0 2013-07-30 15:34 ./foo/bar/
You can pass the --edit option to make any changes to whatever fpm generates.
-pk