I use indexed files in DT in order to maintain the ready ability to find files remotely using SugarSynch. Interestingly, I see there’s an extra benefit to using indexed files - tags placed on indexed items are incorporated into the spotlight searches in OSX 10.9. In fact, using DT to attach and remove tags is wonderfully easy. When tags are added to files that exist only within a native DT database they do not appear in the spotlight search - although they can, of course, be searched within DT. This may be an obvious observation, but I stumbled on it and I find it very encouraging for the further deep integration of DT within OSX. It makes tags that much more useful as a file identification and retrieval strategy.

You might also want to experiment with Ammonite, a 3rd party app that expands on the feature you mentioned by helping browse tags both within DEVONthink databases and within the file system, in one search panel.

(I have nothing to do with the author – I’m just a long-term user.)