It depends if you plan to use that airport or not, after you removed the add-on. If you do, it's best to remove the .INI file, because if you go there with the default airport active instead of the add-on, the INI made for a 3rd party airport might not match the default. But that's not a sure thing either, it depends how many parking spots have changed their names/position from the 3rd party airport vs the default one but, to simplify things, it's best to consider them not compatible.
Remember, when using Navdata, GSX has no way to know which specific .BGL or package contains the active airport, so it's up to you to know which .INI to use.
If you don't plan to return to the airport until you re-enable the 3rd party airport, it doesn't matter, since GSX will never load an .INI unless you enter in range of an airport, and won't scan all the available .INI file either so, having unused .INI files for airports you don't use won't cause any issues, other than taking (very little) disk space.
Instead of remove it, it's best to move it, so you won't have to find it or downloading it again, maybe create something like a "backup" folder in the %APPDATA%\VIRTUALI\MSFS folder to store temporarily disabled .INI files.
