We're in the process of updating the documentation for Zotero 5.0. Some documentation may be outdated in the meantime. Thanks for your understanding.
Direct Access to the Zotero SQLite Database
Zotero uses mozStorage, a database API backed by the SQLite database engine, offering the power of a relational database system within the Mozilla development environment. All system data and item metadata is stored in an SQLite database, zotero.sqlite, within the Zotero data directory.1)
However, external access to the SQLite database (including direct access via the mozStorage API) should be done only in a read-only manner. Modifying the database while Zotero is running can easily result in a corrupted database, as mozStorage caching breaks the normal file-locking in SQLite that allows for safe concurrent file access. And even if Firefox is shut down before accessing the file, modifying the database directly bypasses the data validation and referential integrity checks performed by Zotero and the Zotero server that are required for Zotero to function properly. Generally, the SQLite database should be viewed as an internal database that has the benefit of being externally readable for people who want to get the data out in other ways.
Also be aware that the SQLite database structure can change between Zotero releases.