I've just discovered that when using

SchemaExport export = new SchemaExport(conf);
export.drop(false, true);

generates random foreign key constraint values to drop and does not use the constraints that are existing in the database. This means that I cannot drop the db anymore, so I had to move back to Hibernate 4.2.0.

Test case:
use random existing DB, try to execute drop script and you will receive sql errors while removing constraints.