I'm not a HDD expert by any means, but there are many processes that access your HDD for multiple reasons from performing housekeeping to providing important system info. smartd is only one. updatedb is run regularly by cron to keep your mlocate.db current so that the locate command can find files for you. There are likely others that I haven't learned about.
To track what processes these are over time, you need to install iotop from the repositories and run it in batch mode.
iotop must be invoked with sudo and run as root. In batch mode, it will log I/O usage over time. Reviewing the log will help you determine what process(es) is accessing your HDD.
sudo apt-get install iotop
I would find the missing reassurance of smart monitoring and the missing functionality of locate an unacceptable price to pay just for spinning down a HDD, but that's just me. If you want to hobble these functions for the sake of a quiescent disk, it's your call.