There is some usage of no:brand=yes for off-brand or unbranded stuff. I suppose that’d be one way to indicate an independent shop, but I wouldn’t be surprised if there are already other tags for that.
no:brand:wikidata=yes on the other hand would mean that it is part of a brand, however small, but there’s no Wikidata item about it. I’d probably avoid tagging the nonexistence of a Wikidata item, because it could easily get out of sync when someone decides to create an item about it on Wikidata.