The short answer is that a national judge's ruling doesn't directly affect other countries, although it could indirectly affect them if it leads to an appeal to a European court and their ruling clarifies the law in a way which is incompatible with other countries' implementations.
The longer answer: EU law works by means of "directives" which each country then implements in its national law. Each directive comes with a deadline to implement it, although typically most countries miss the deadline. But in principle the European Commission can sue a country which fails to implement a directive, and fines can be levied. The issue here is that the Dutch implementation of the Data Retention Directive went further than the minimal requirements, and the judge has ruled it incompatible with other European law. (It's not clear from either of the articles whether that was the Data Protection Directive or the European Convention on Human Rights*).
The two main options now would be that the Dutch government appeals to a European court (the European Court of Justice if it was the Data Protection Directive that formed the basis of the ruling, or the European Court of Human Rights if it was the ECHR); or that it passes a replacement law which sticks closer to the Data Retention Directive. If it doesn't do either of those, it would be failing to fulfil its obligation to implement that directive.
* Not EU law, but I think all EU countries are members of the European Council, and the most recent constitutional treaty of the EU commits the EU as an organisation to acceding to the ECHR.