Move the documents into the database, then move them back out to the external folder again. DEVONthink always writes the tag info out to the filesystem only when it writes the document to the filesystem. In other words, if you change the tags in the future then you will need to move them into/out of the database again.
As a tip, you can streamline this process by using a smart group with the criteria ‘All of the following are true’, ‘Kind>Is>Any document’ + ‘Instance>Is>Indexed’. Then select all the documents in the smart group, then right click>Move Into Database. Once everything has moved into the database, right click, Move to External Folder.
OT but related – if what you’re looking for is the ability to browse or lookup tags, for files in Finder and for files in your DEVONthink database, then check out Ammonite, a simple (not expensive) toolbar app that will browse for files with a combination of tags, filetype, and date (created or modified) – in both Finder and DEVONthink.
No, the documents will be exported back out to same Finder location they were in before.
My understanding is that it is all about performance. DEVONthink databases are structured the way they are to maximize performance. The more that DEVONthink has to write outside the database to the filesystem, the slower the performance.