You should be fine closing it & then next time you open Cubase you can change your settings in Mediabay so it doesn’t scan your Kontakt sample libraries.
Oh, but it DOES, actually Mor me C6 has done this annoying updating several times, and me neither knew that what the hell it was supposed to even be. Very frustrating when you are closing your PC after mixing for straight 30 hours and would like to get some sleep for a change, and then you have to stand by and picking you head with match sticks under your eyelads for an hour so that it will close