I'm running a 2014 iMac 5k and first noticed this issue with my external USB hard drives plugged in (2 Western Digital My Book drives). When I set the Mac to sleep at night, the external hard drives spin down as well, until a second later when they spin right back up again. I started just unmounting the hard drives and unplugging, inconvenient but not a total pain. But I noticed that I still hear my internal drive spin up as well (1TB Fusion drive). It's usually at somewhat random intervals for only a few minutes at a time. I've disabled "Power Nap", "Wake for network access", and enabled "Put hard disks to sleep when possible" and still have the issue. I've also added the external drives to be ignored by Spotlight. Not sure what else could be going on. Any ideas?