Is there a way to use the wonderful annotation script (or a variant thereof) to annotate a bookmark or a linked (not imported) document?
As far as I can tell, the answer is negative, because the annotation script replaces the URL of the bookmark (or linked document) with the URL of the annotation.
Try the updated script that Eric posted in this thread. I have not tested it with indexed files, but I can confirm that it will not blow away the URL of a bookmark.
I found a (partial) solution. It works only with links to locally stored documents: Create an alias in Finder (or, in the case of a local DevonThink document, a replicate) and use that as a “link” of sorts. Unlike bookmarks, the aliases/replicates can be annotated normally.
The question is still open, however, with regard to bookmarks.
UPDATE: Thanks, Greg! Your message arrived as I was typing this post.