ad John Smith's uniqueness:
I think that derby's data structure exactly reflects described situation. Once you have two or more J.S. _without_ some related rows in other tables, you really cannot distinguish between them. But it is not disadvantage of derby's normalization, it is lack of informations. You can, for instance, add some external (real) unique identifier into database table Person (insurance number? passport number? e.t.c.)
ad other:
I don't understand exactly what do you need. But I think that you can create some database views or some more complicated (perl) structures representing derby's data structure in proper format...
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