It's normal that airport won't appear in the GSX config panel, because the only thing that panel knows are:
- Jetway replacement files that comes with GSX, about 900 files, one for each airport that have jetways in the default scenery.
- Airport services that comes with GSX, to replace default ground vehicles, for all airports with at least 5 parking spots, about 15000 files.
So, clearly, an airport that doesn't exists cannot possibly be part of files that come with GSX, that's why it doesn't appear there. To remove such airports, you use the Airport Visibility option, explained in the manual at Page 60.
In your case, the lie will be like this:
airport_visibility_LIFN = 0