It is possible to configure the harddisks to spin down after a period of inactivity, but if one or more processes keep reading and writing from the disks, that will prevent them from entering standby mode.
To find out which processes are causing disk activity, the following script is very useful:
blkdevMonitor.sh
The script works like this:

• A standby signal is sent to the disk.
• Wait until a process wakes up the disk and then prints out name of that process.
• Repeat.

The following link contains a list of daemons and configurations known to cause random disk activity: Standby Mode FAQ
Older versions of Squeezebox Server caused lots of disk activity, but fortunately that has been resolved in version 7.5.1.
What is jdb2 and flush?
Sometimes the processes “jbd2” and “flush” are waking up the harddisk. As I understand, these processes are responsible for doing delayed writes to the disk in order to optimize performance. In other words, they are writing to the disk on behalf of other processes which makes it difficult to find the culprit(s). In my case, it was the samba daemon accessing the disk. As long as a PC or media streamer on your network has an open view on any of your samba shares, it will cause the disks to wake up.