I don't know many things on data encryption, however I think there are various solutions either (mostly) at the operating system level / application level, or the hardware level (as far as I know, there are controllers that support encryption).
GParted doesn't provide any such solution.
Concerning the windows backup, I don't understand well what you mean by GParted partitions.
GParted doesn't create any partitions for it self on the storage media. It creates partitions with various file systems, that are used by the various operating systems. The "windows backup" can do backup from the file systems that it understands, i.e. fat, fat32, ntfs and, I guess, the newest fat64. This is valid if the filesystem is consistent (not damaged) of course.
In case of Linux partitions on the same system (ext2/3/4, reiserfs etc), the operating system doesn't understand them and doesn't mount them without some special additional software. Even in this case, I don't know at all if the windows backup is able to backup files from an ext... partition.
*** It is highly recommended to backup any important files before doing resize/move operations. ***