I think that is exactly your problem. I have stock firmware, and have nothing enabled (no torrents, download master, media server, etc.) Nothing. But the drives spin 24x7 on both USB2.0 and USB3.0.
After digging around to find out what the problem is, it really has nothing to do with your RT-AC68U router. It has to do with the stock ASUS firmware, and everyone with ASUS routers is complaining about it.
I think the only solution to this is to install Merlin firmware, then there is an option to spindown (or sleep) the hard drive after a certain interval of inactivity.
The reason I came here and signed up for an account was to download the Merlin firmware to update my RT-AC68R router to fix this same problem I am having. I want to connect USB harddrives, but don't want them to spin 24x7 and burn out after 6 months.
The RT-AC68R I have is identical to the RT-AC68U you have. "R" for retail store like BestBuy, and "U" for online store like Amazon, Newegg, etc. Otherwise, identical. So I think it is the same problem.
I'll let you know how it goes once I upgrade to Merlin tonight, and select the setting to spin down the drive after say 10 minutes of inactivity.
I'm not sure why ASUS doesn't add a switch setting to spin down and sleep the drive to the Stock Firmware. But I figure I'll just install Merlin and see if that solves the problem.