Well, I took the plunge and tried it. No problems so far.
Mind you, I'm not trying to use permissions at this point. There are only two restricted directories which contained system backups but since eBox has been, for the most part, living up to my expectations, that system is likely never to be used again, it's largely irrelevant.
By the way, when you check the permissions on an NTFS drive, the system reports that "the permissions could not be determined", so obviously, if I do want to restrict user access in some way, I'll have to get another drive and format it with ext3.
Now, does anyone know if the ext3 file system will work with Western Digital's WDTV device?