The nginx installed from the bootstrap.sh (deb http://ppa.launchpad.net/nginx/stable/ubuntu trusty main) is not HUPping the process. It's invoking invoke-rc.d nginx rotate which is not the appropriate command on ubuntu.

root@dokku:~# invoke-rc.d nginx rotate
initctl: invalid command: rotate
Try `initctl --help' for more information.
invoke-rc.d: initscript nginx, action "rotate" failed.

I noticed because I have a tail -F /var/log/nginx/*.log and when I came in after the weekend tail showed the files being changed, but nginx was still dumping to the old rotated logs.