In my experience it has always been the case that when you deselect a folder in Dropbox’ advanced preferences that that folder and its contents disappear from your dropbox folder on your mac (by ‘always’ I mean: ever since Dropbox features selective sync).
However, I have the impression that the original poster is not talking about the appearance of the DEVONThink folder in the Dropbox folder on his or her mac, but rather about its appearance in the selective sync menu of the Dropbox preferences:
This is unusual or new and a bit strange isn’t it?