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The Story HD supports browsing by folder structure, and Calibre can store files in a (very customizable) folder structure. That's what I use with my Story HD and I like it much better than the flat DB view.
This is just guesswork but, as for the database, I think it won't be easy to do. Although the database files are accessible in the internal storage of the reader, the format seems to be proprietary, and it also seems to have changed between firmware versions (newer versions now also store the font size in there, I think).
Then there are known cases where the Story HD device hung completely due to a broken DB file and at that point the device is bricked as you can't access the storage through USB anymore and there is no reset facility. So playing around with those database files could be dangerous.
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