1) Yes, the permissions will be messed up, Windows has no conception of UNIX file permissions. It will break horribly
2) You can use rsync to mirror directories efficiently. What you should actually do, of course, is have /home on some kind of RAID set and back this up to DLT.
Just as a general point, any kind of "backup" system that does not involve ejectable or removable media is _not_ a backup system.