I have no idea if it's a QNAP-wide issue, or just some specific models, I haven't bothered to do that much research. I'm guessing that the discs WOULD spin down if you have that option selected if they weren't constantly being pinged a couple times a minute. That constant pinging is the part I can't seem to track down.
An excerpt from a post I was reading while researching this sums it up prettt well: "700 posts about spindown/sleep/standby not working in the QNAP HDD Spin Down Forum. No one seems to be able to resolve it. Qnap clearly couldn't care less."
The only solution that I've found that seems to work is to install some other operating system on it, which kind of defeats the purpose of buying a turn-key NAS, and is slightly outside my comfort zone right now. I just ordered a kill-a-watt, so I'll see how much power it's taking with/without drives and go from there if it's worth my time to dive into an OS swap, or building a custom rig.
They run a custom vendor-locked distro named QTS, so they're not really as easy to modify as a normal system, I don't think you can even install programs like that.
I'll definitely bookmark it though if I ever get around to building my own solution, thanks!