Can upgrade to Mavericks harm Bootcamp NTFS data partition?
Usually OS X backups don't mess with the partitions, except for when they create a recovery partition. And since your recover partition has been (manually?) removed, OS X will probably try to add it again.

If you do the upgrade, definitively back up all your stuff (on the windows side as well!).

If you want to play it really safe:
1 - get an external (usb) drive
2 - copy your mac-partition to that drive (via disk utility or any other cloning software)
3 - boot from the external (usb) drive and run the update there
4 - clone the partition back form the external onto your internal drive