The file system is the best way to store attachments imo, the database means a hit in preformance.
Backing up the attachments when stored in the file system is as easy as backing up any directory on your web-server.
The upgrade path from vB 2 to vB 3 requires attachments in the database, because this is how they where always stored in vB 2. There is a hack to store vB2 attachments in the file system, but even with that when the time came to upgrade to vB3 you would have to move them back to the database.
You have a large attachment table, one of the largest I have seen. I heard reports of people having to keep the browser window open for 2 - 3 days for 3 gig's of attachments. So my advice is to leave the browser window open and hope it dose not eat the new harddrive
Maybe you should contact offical support about this one, they deal with many large boards daily with these kinds of issues. I rarley work directly with large forums