I have the GroundTraffic plugin in my main plugins folder installed. Do i still need the GroundTraffic plugin folders in sceneries? I have way too many sceneries, which are containing the GroundTraffic plugin and they are all listed in the Admin Plugins menue. So is it safe to delete the GroundTraffic plugins folders from sceneries and just keep the plugin in the main plugins folder? 

Nope, you can't just keep the main plugin. Unfortunately the plugin has to be in every single scenery which uses it.