For large data repositories, especially public/open datasets, a major concern is versioning. While it is not impossible to render a nice diff between two SQLite files, it's not as ingrained in our everyday tooling (e.g. GitHub) as plain-text diffs.

For small to medium-sized datasets, a nice middleground would be SQL dumps. Put the dumps in Git for versioning and diffing, and load them into $DATABASE for actual queries.