SQLite is a "database of last resort". It's good for prototyping, and for bundling with applications cos it requires no setup, but most of the time I'd prefer to use PostgreSQL, MySQL or a "grown-up" database like Oracle.
Implementing your own primitive bucketing algorithm by using several DBM files sounds ... perverse. If going down the DBM route, I'd use just one file and let perl handle that. I'd also use GDBM_File in preference to DB_File as it has fewer restrictions on your data. You might want to consider DBM::Deep if you want to fake up a filesystem in a file, or go crazy and create a *real* filesystem in a file, optimised for your circumstances, and mount that.
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