If you decide to go down the DB File path, one option that you can definitely consider would be using the MLDBM module. The MLDBM module lets you store a multi-level hash structure in a single level tied hash.

Basically it would eliminate the need to store everything in seperate DB Files. Of course, the tradeoff is that it becomes really slow with large datasets. However, I think that 1000 records would be small enough.