It seems the intrepid pair had acquired certain confidential files concerning big-time crook Mink K. (I thought Mink K. sounded like a hip-hop artist, but remember that the papers here always refer to a defendant by last initial so as to protect his or her anonymity). After the Telegraaf published an article about Mr. K., the AIVD (the Dutch intelligent service, like the CIA but with domestic jurisdiction as well) began a so-called Class A investigation into the two reporters. This is the most intensive type of investigation, and it involves having the targeted individuals followed and their conversations bugged/tapped. The judge told the AIVD to cut it out.
From the news report I read, it seems that freedom of the press wasn't the issue; in principle, the judge's reasoning would apply to any two individuals who served as mere conduits for the classified information. The decision (I think) was that as mere conduits who had made only a limited use of the files, the two reporters hadn't done anything serious enough to warrant Class A treatment.
Maybe it's somewhat akin to the U.S. constitutional law of probable cause. The federal Supreme Court has demarcated a couple of levels or suspicion for increasingly intrusive kinds of searches. If you need a warrant, you have to show probable cause (it says so right in the Constitution). But the Court allows a "stop-and-frisk" under lesser circumstances.
The New York state courts have an even more elaborate hierarchy: the police need this good a reason to ask a person to stop and answer a question, a bit better reason to stop and frisk, etc.
If I've got it right, the Dutch court was saying that there wasn't a good enough reason to follow these guys and tap their phones, but (a) a less intensive investigation might have been OK and (b) the AIVD could in principle conduct a Class A investigation of journalists if there was a good enough reason in the particular case.