I will use exiftool for geotagging many pictures using a kml file. Is there any option on command line for tagging only pictures without any existing geotag? I do not find any information about it.
I would simply check to see if there already was a Latitude (or Longitude) by adding -if "not $GPSLatitude" to your command.
Change double quotes to single quotes if you're on Mac/Linux.
Another option would be to instead add -wm cg (see the -wm (-writeMode) option). That means that exiftool will not overwrite tags that already have data.