Where do closed notes in OS X Notes app go?
Well, this seem to be down to my unfamiliarity with the Notes app. As in "Mail" there is a browser overview under Window > Notes (Cmd-0) (in my language anyway) and any closed notes can be found there. 
Despite a long long use of OS X apps this didn't feel like a natural place to look, but it's logical considering other Apple apps. I think possibly "Note browser" would have said more about the function of this menu option. I must have understood this as a reference to the app itself.