A reason to keep tags external in 'entry as file' blog engines
In EntryAsFileTagProblem I ran over the problem 'entry as file' blog engines have with tags (because they need efficient two-way queries on the mappings between tags and entries) and suggested that one solution was a completely external mapping file (or files) of tag information. I've since realized that there is an additional reason to like this approach.
Put simply, having tag/entry mappings in an external file allows you to change the tags associated with an entry without editing the actual entry's file; especially you can retrospectively add tags to old entries. This is based on my feelings about two issues (feelings that other people may not share).
First off, I think that a decent amount of tagging is probably going to be done after the initial publication. Tagging is taxonomy and sometimes it's only going to be obvious when you write the second (or third, or whatever) entry that touches on a particular thing. In addition I'm biased against single entry tags (they're not merely pointless but distracting) so I'm not even likely to put in obvious tags unless I'm relatively confident that I'll write at least a second entry with the same tag.
(Fundamentally tagging as exposed in a blog is about luring people to read additional entries by giving them a way to follow interests. If you're interested in a particular tag, you can find and read other entries that have that tag. If there are no other entries when you click through the tag's link, I've wasted your time. I can use single-entry tags internally for tracking or taxonomy purposes, but I shouldn't expose them to visitors.)
Second, I'm strongly biased against modifying entry files after their initial publication; I would like to do it as little as possible. If the master source of tag information is in the file and it's common to modify tags after publication, well, I'm going to have to edit entry files much more than I'd like. Putting the same information into a separate set of files is less problematic this way.
(One issue with editing entry files is that it opens you up to making larger edits than you intend, because the tag metadata is mingled with other metadata and the actual entry text. No matter what you do to a tag metadata file, it only affects tag metadata.)