External hard drive spinning up during sleep
Solution 1:
Unfortunately, Mac OS doesn't eject hard drives when the machine enters sleep. And since your MacBook performs some "activity" during sleep, a writing/reading process might keep the hard disks awake.
There are at least three solutions to this problem:
A) You eject the hard disks each time before you enter sleep
B) You get the Jettison App for $4.95 (http://www.stclairsoft.com/Jettison/), which automatically ejects hard disks before the MacBook enters sleep, and mounts them when the MacBook awakes. There is a 15 days free trial if you like to check if it works for you.
C) Disable the Power Nap mode
Solution 2:
Try with disabled Power Nap mode!
In system preferences energy saver.
Here is my setting, but I do not have an external HD to check that.