I am pretty sure Debian installs and runs smartd by default to keep an eye on your disks' SMART status. The regularity with which the disk is spinning up certainly points to something like that.
First, run /etc/init.d/smartd status to check whether smartd is running. If it is, that might be it. If not, it's something else, and you can disregard this answer.
Second, check /etc/smartd.conf and /etc/defaults/smartmontools. The best way to have a normally-powered-down disk in a smartd configuration is to list it manually in /etc/smartd.conf but with a -n switch given. For example:
/dev/disk/by-id/wwn-0xXXXXXXXXXXXXXXXX -a -l error -l selftest -n standby,10,q -m root@localhost
The -n (or --nocheck) is described in the smartd(8) and smartctl(8) man pages. standby here specifies don't check the drive (which may spin it up) if the drive is in standby mode (spun down), and ,q means don't write an informational log message saying that the check was skipped (which itself may cause the drive to spin up). You can also add ,N to this where N is an integer specifying the maximum number of consecutive checks to skip. In the example above, after ten checks are skipped the drive will be checked anyway, regardless of its current power state.