To this point Spotlight is not officially supported. Using custom mount flags, some users managed to get it partially working, but this is nothing we can offer support for yet.
I can not answer any of your questions. The notification came from the operating system which decided to ask you when it noticed there was a new drive. I have no idea what triggered this. Cryptomator does not nudge Spotlight to attempt this in any way.
Also, using a quick search I didn’t find any clear instruction on how to revoke granted access rights from Spotlight. Of course there is the blacklist that you can add folders to under System Preferences → Spotlight → Privacy. Who knows, maybe the location would have been added there if you chose to deny access when Spotlight asked you. 