Sorry, I can’t recommend such an app, but maybe others can.
Personally, I would like to see this feature in MarginNote itself. I gather it uses a SQL database for storage, so complex searches should not be complicated. In this regard, Bookends is exemplary. The whole idea of using a bunch of different apps is not very appealing. Already I have to use Acrobat to prepare PDFs for MarginNote and some other app for organizing notes. Fewer apps in the workflow sounds better than more.
FWIW, I recently showed MarginNote to a researcher-friend. She was initially impressed, and then asked about searching, and whether it was possible to search for several different terms and/or a hashtag together. When I said that MarginNote didn’t have a good way to do this, she immediately and totally lost all interest. (Developers, are you reading this?)