IFD0 is one directory in the EXIF information. ExifTool does not zero this.
You may be referring to the problem where some tags are duplicated
between the ExifIFD and IFD0. ExifTool will remove the duplicate tag
if it exists when you are writing that specific tag. However, no information
is lost since this tag exists in another location (and it really shouldn't
have been duplicated to begin with). I'm not sure that NEF images have
this duplicated tag problem anyway.
I always recommend keeping backups of your originals, but there should
be absolutely no information or image loss when editing NEF with exiftool.