I was especially thinking about a program running on a server. I wouldn't statically link everything for a desktop program, because it just causes incompatibilities left-and-right. But for a server, you don't have external vendors, so this is a good option, and if you use SQLite as the database, then this means that deploying is not more complicated than uploading a single executable and this is also something, that can be done atomically.

I don't see how this has worse effects on recovery and availability. The data is still in a separate file, that you can backup and the modification still happens through a database layer which handles atomic transactions and file system interaction. The availability is also not worse, unless you would have hot code reloading without SQLite, which seems like an orthogonal issue.