The number of records don't matter do they? And DB2 supports auto generation of keys so
you should be able to add a surrogate key without being too disruptive. The problem you will possibly find is where the developers of other applications have been sloppy and not named the attributes in insert and select statements, at which point they will fail.
If its too much risk to fix the data model then you will have to use native SQL from Hibernate rather than trying to map an object that is not relational.
Adding primary keys should be in your DB2 documentation.