This depends on the version of Ghost that you have; prior to GSS2 you could delete files in NTFS images using Ghost Explorer, and in GSS2 you can edit NTFS images fully just as you can with FAT ones.
When you in-place edit an NTFS image, any edits you make are done by adding additional instructions to the end of the image, so deletions don't actually remove any data (and so make the image smaller) until you "recompile" the image using the File menu in Explorer.
You have for some time (I think in GSS1.0 and GSS1.1) been able to script other changes to NTFS images using an extra tool we made called
omnifs, which can run in DOS alongside Ghost and can do all kinds of things to an NTFS filesystem. In GSS2, we've also added a 32-bit Windows PE version of this tool called
omnifs32, so for any editing tasks that go beyond what you can do in Explorer you should be able to script up something with those.