I have found [better-sqlite3](https://www.npmjs.com/package/better-sqlite3) to perform much better than [sqlite3](https://www.npmjs.com/package/sqlite3) on one of my project. They advertise [that speed](https://www.npmjs.com/package/better-sqlite3#how-other-libraries-compare) and also have [better docs](https://github.com/JoshuaWise/better-sqlite3/blob/HEAD/docs/api.md). If you are interested in switching, I could work on the PR, let me know. Note: https://github.com/mapbox/node-mbtiles/issues/96 might be related.