Not necessarily sqlite, but rocksdb is looking like promising option for foundational storage system. You have things like zenfs which runs rocksdb directly on nvme storage, and then you have lot of higher level systems on top of it like Cephs BlueStore and mysql/maria MyRocks. It is not much of a stretch to imagine whole OS built around it
What is notable here is that it would be both better aligned with how the underlying storage hardware works, and simultaneously also offers more usable interface for applications.
It is pretty apparent that the biggest reason why we commonly use posixy files is inertia rather than them being very good fit for anything these days