Zip files use a well documented, easily-reproducable and widely implemented deflate algorithm. It's reasonable to assume that someone could, 100 years from now, unzip an OpenDocument file. The contents are XML files - basically text - which can be read with any simple text editor and parsed. The XML is also at least somewhat self-documenting regarding the contained document.
SQLite databases have a binary format which is known to change periodically. An attempt to read a SQLite file in 100 years would have to know the exact version of the file, and be able to reach back through history to find that version of SQLite (or a compatible version), and find a way to compile it for whatever CPU architecture exists in 100 years.
This could be mitigated by including the appropriately versioned documentation of the binary format with the database itself - however to the best of my knowledge, full documentation of the binary format (outside the code) does not exist. The end product - a relational database - would also be less self-documenting than the XML version.
IMO, it would be much better to keep the inefficient zipped XML files.
[EDIT]: The binary file format: https://www.sqlite.org/fileformat.html
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