To be clear, I do not use the script. The USB stick is mounted all the time, and DSM5 will hibernate with it mounted. It will also WOL/sleep with it mounted.
From experimenting, it seems that it is the packages that prevent it hibernating, not a USB stick being mounted. From Googling, hibernating, or lack of, seems to be a general issue with Synology, not an issue specific to Xpenology or DSM5 - http://www.synology.com/en-us/support/faq/568
Why not do as I did/am still doing, try stopping all the packages and see if it hibernates. If it does, turn them back on one at a time to see which cause a problem. For me Sickbeard seems to be a problem, so I am experimenting with setting up a schedule to run it, so instead of it searching every xx minutes, I stop that service, start it on every xx minutes for it to do its stuff, and then stop it again. So far that looks promising. It still finds and feeds things to SABnzdb, but the machine hibernates when it isn't doing so.