Hibernate is an Object/Relation Mapper, so your entities will be mapped to database tables. There is no need to store entities to files when you can use a lightweight database like HSQLDB which has disk persistence as well. All in all, your entities are basically stored in some files on disk, just that in a compacted binary form.
Because of the
ACID guarantees, SQL capabilities, Indexing options, and
in-memory buffer optimizations, a database is way more suitable than a plain text file even for trivial tasks.
You can also use JSON, and, this way, your Domain Model is not strictly tied to a fixed schema.