Well, if you think about it, the Windows registry already is a hierarchical database – just a quite limited one. You could have a hierarchical database with richer features (LDAP is a good example of that, although in some ways LDAP is rather clunky).

If by database you mean "relational database" – I'm not sure the relational model is the best fit for a config store. I think a more hierarchical database model is more natural for that purpose. (Of course, you could use a relational database as an underlying implementation detail – LDAP is fundamentally a hierarchical database, but there exist LDAP servers which store the data in an RDBMS, for example Oracle Internet Directory.)