It is in fact a rather surprising decisions, since Dutch judges have no tradition of ruling in 'contra legem' procedures; they are in fact forbidden by the Constitution to do so (article 120 says judges shall not judge the constitutionality of laws and treaties).
Now, the loophole here is that treaties are considered higher law than the Constitution, so judges can rule local laws in violation of a treaty. They don't tend to do that in mere district court though.
Apparently the case made by complainant was compelling enough, and the governments argument weak enough, that a mere district judge felt they could safely make that ruling.
 On the gripping hand, the principle of subsidiarity means that if a case is covered by the Constitution as well as a treaty, judges are supposed to use the Constitution as the basis for their decision, once again invoking art. 120. But of course if the Constitution and the treaty align enough, appealing to treaty law wouldn't work anyway.