What is Notes.app's iCloud notes database location(s) for recovery (El Capitan)?
This is not a direct answer to the question "What is Notes.app's iCloud notes database location(s)" but it might be useful information for others who need to recover an iCloud-synchronized note. 

Given my lack of success with everything I tried I called Apple support. They were very helpful and after a few unsuccessful attempts replacing folders they looked into my iCloud account and found that on their end there was "one recoverable item" that showed up. After verifying my identity they could then "recover" that item and, voila, the missing note popped up in the notes app under Recently deleted items. It had been deleted beginning of September. Had I only known it was that easy ...

So it seems that deleted iCloud notes are not permanently deleted after 30 days and still recoverable by Apple. I forgot to ask if forever, or for how long ... 

In any case, while I've resolved my problem I'd still be interested in the actual location of the iCloud-notes database. So if anyone comes across this at some point and finds the answer it'd be highly appreciated.