I can confirm this issue against 5.2.10.Final. I do configuration using a hibernate.cfg.xml which works in principle (application connects to database, so hibernate reads the configuration at least).

I tried to override methods from PhysicalNamingStrategyStandardImpl via hibernate.cfg.xml with

        <property name="hibernate.implicit_naming_strategy">org.hibernate.boot.model.naming.ImplicitNamingStrategyJpaCompliantImpl</property>
        <property name="hibernate.physical_naming_strategy">dbla.dbla.services.database.PhysicalNamingStrategyImpl</property>

Using a step debugger, I figured out hibernate still uses PhysicalNamingStrategyStandardImpl because its methods were executed whereas the overridden methods were not.