When you “close” the NNC window with the X, the NNC still runs in the background in your tray
The “Quit” would close the application completely. In the “Launch Options” you can set if the NNC will be started automatically in the background when the computer starts. This is the default case and also the recommended one. When the NNC runs, and you add a package via the re-order tool in the sim, the NNC re-prioritizes the packages automatically so that the navdata package is always on “top” (means with the highest priority-number).
You would loose these feature, if you “Quit” the application and/or you don´t let the PC start it during the startup phase. So, it´s highly recommended to leave as is. The app itself needs only a few kB memory and has no performance impact on the sim or other application.
Correct - under normal conditions you don´t need this file. I see this now more for developers rather than for end-user.
The only “negative” effect is, that you can´t enable/disable a package any longer as in the past with the “active”-attribut because this attribut doesn´t exist any longer in the new content-file. So, when you want to disable a package, you should do this directly in the sim in the content-manager, or move it out of your community folder. It is a pity they took that out but on the other hand, it´s a clear “message” to the end-user not to hack this file manually 
Cheers,
Richard