Since this thread is being noticed by someone, I'll post my findings up to this point. No, s3 sleep does not have an option that allows for shutdowns when the disks are still spinning. However, Unraid keeps a record of all disk reads and writes in /sys/block/$DEV/stat with $DEV being the disk name. You can find an array of all hard drives (not cache) by running var=($(grep -PA1 '^name="(parity|disk)' $ini|sed -r '/^--/d;/^name=/d;s/"//g;s/^device=//'))
var will contain all DEVs of the disks that are not cache. Then you can do a for loop like so DEV="${var[index]}" and append the contents of the file in /sys/block/$DEV/stat to a variable for each DEV in var. Sleep for a few seconds then run the loop again, except with another variable. Compare the two variables. If they are equal, no disk use. If not, the disk has been used (read or written from).
If you want individual disk stats like write only, you can look into /sys/block/$DEV/stat and adjust your script accordingly (it has all info about disk reads, writes, ioticks, etc.) You can find documentation on it as this file occurs in many linux distros.
P.S. Tested the script and it works!