I am already using the no-resolv option and the ls -la /proc/<pid>/fd gives me only sockets and pipes apart from the log and lease files.Not sure what is waking up the disks then. Maybe the NAS is not smart enough to know that dnsmasq accesses the files on the USB mount and just wakes up the disks for any file system access.
perhaps you could stop nsdmasq for a short while and see if the disks stays sleeping ?
matt