Some applications and utilities come with extended facilities to view and manipulate files, regardless their visibility status. The app cannot do anything to prevent this situation (as any other app that we are aware), since this could lead to dangerous scenarios as system stability issues. The app provides a simple interface to deal with the OS X System visibility property and does not patch it or interferes with the System performance.
The same applies to the Finder: the app relies on the Finder services, and does not modify any of its internals. Whether you need advanced levels for protecting your data there are other ways as protecting information on removable media or using OS X FileVault. To learn more about Protecting information on removable media and on OS X FileVault open OS X Finder’s Help.