While this is not a perl question, how does storing these files in blobs impact your database recovery procedures?
From what I understand, MySQL does have a (slightly crude) recovery method -- the database keeps an update log of all activity. You can then replay the update log which stores the changes since your last database backup to bring the system "up to date". (Although I have not played with this, I also assume you could edit the update log to simulate a point in time recovery.)
It would seem that storing just the file names (assuming you do not have version control in place for the documents) means that you would have a very difficult time recovering from certain failures. However, (as I mentioned earlier, I have not played with the MySQL update logs) it would also seem that storing the changes to multi-meg or multi-gig fields would cause the update log to exceed the OS file size limitations.
How have these concerns impacted your implementations?