Yeah, a lot of people store them in the database, and I really don't understand why. Eleven years ago? Who knows? ha ha! Could have been plenty of reasons for doing it back then.
The nice thing about having a separate directory is that you can back those things up separately. Database corruptions, etc., aren't going to affect everything. I have personally seen so many forums/images/etc., get destroyed when the database gets corrupted. On any forum, I basically back up the database, back up the entire forum directory (for a lightning fast re-install should something happen), and then back up the images/avatars/etc. directories again separately. Makes it really easy to fix something should an upgrade go awry, and I have had plenty go awry.
But, what do you mean by "afterward, update the new images manually"?
I'll go through the images (for the forum software...vBulletin, for example) and update every image manually, so I know they aren't going to overwrite something I have changed, or some custom image I use for the forum, etc.
So my forum update procedure looks like this:
1) Update Database
2) Update forum files (minus images)
3) Update /images directory.