Will running home from NTFS be a problem, or perhaps a performance killer?
- Yes, NTFS does not understand Linux permissions. If you're using Gnome, then you won't even be able to log in due to permission issues.
dot files on NTFS are not considered hidden files and due to the lack of permissions -anyone- can change those files without having to worry about passwords.
Also read this: http://en.wikipedia.org/wiki/NTFS#Linux
Due to the complexity of internal NTFS structures, both the built-in 2.6.14 kernel driver and the FUSE drivers disallow changes to the volume that are considered unsafe, to avoid corruption.
If you want to do it like this you are better of with FAT. But WHY break the security of a Linux system? Why?
A better way is to put /home on ext3 or ext4 and mount the directories from the Windows partition (in that case you can use NTFS though I still advice against it). This will not break the security model but you can still share all your personal files.
Can I convert the HDD from NTFS to ext3 (or ext4?!) without losing all the files, and how?
GParted can do this. But it is probably quicker to move all the files elsewhere and then format the disc and copy the files back.