Brian Pepin, Programmer on the Xbox One system software.
Written 10 Apr 2015
I helped write the external storage feature. Unless the console is actively updating games on your external drive, there is no code that periodically wakes it up while the console is asleep.
When we first started working on the external storage feature we wanted to make sure you could use any drive that "qualified". We didn't want to benchmark drives or have a white list of approved drives, so we simply allowed any drive over a certain size that could connect at USB3 speeds to qualify. The thought was that these hardware requirements would rule out older (and probably slower) drives by nature of USB3 being fairly new, and by nature of our size minimum being impractical to implement in a cheap USB key.
What we found was a huge variance in USB behavior. Drives would be sold as USB3, but use either substandard chipsets or very cheap cables that would prevent them from reliably connecting. Sometimes cables were so poorly shielded they would not work in the side port of the console because it was too close to the WiFi antenna. Lots of drives had a hard time properly responding to USB power management requests. Power management problems with drives were so commonplace that when we sent out the first software update with external storage enabled we forced external drives to stay fully powered, even in standby. Only later did we add an option in settings to allow them to power down, and only after that did we finally switch them to power down by default.
It sounds like you may have a drive that isn't happy about powering down. The USB ports remain powered in standby and it is up to the drive to listen to USB power requests and power down. Your drive may not want to do this. You are correct that constant cycling of the drive will eventually wear it out faster. You can reach a middle ground by changing the option in settings to leave the drive powered all the time. The drive will last longer constantly rotating than it will starting and stopping all the time.
If you still experience this cycling while the "keep the drive powered" option is checked, please submit a post to the Xbox support forums (Xbox One Console). Include the make and model of your drive. Microsoft support engineers regularly check the forum and may be able to confirm your drive model as problematic or may be able to reach out to you for more information about your console.