Actually no. I'm still learning the system.
I read from man pages:
man rc(8)
rc.d/ is the directory which contains various sh(1) scripts, one for each
service, which are called by rc at startup, rc.shutdown at shutdown, and
as necessary during system operation to stop, start, restart, reload, or
otherwise control the service.
I understand this that rc calls every service from rc.d/ although rc.conf or /etc/defaults/rc.conf wouldn't have any entry to that service.
But yes I added smartd=YES now.
I have btw default full installation and /etc/defaults/rc.conf don't say anything about smartd.