I see a list of different version of publications in PUBLICATIONS table of the broker DB which have already been deleted from Tridion Docs CMS. So I don't have the unpublishing option for those publications. Is there some Database query to clean up the Broker DB?
I believe, in this case, the best option you may have is to contact customer support, who can provide you with a supported/approved sql query to remove this data from the broker DB.
Alternatively, you could create a new empty broker database, republish everything that is currently published, and switch your current db (containing the old publication data) with the new one. This might off course only work for you if you don't have a large amount of items to republish.