The key point is that state secrets can only be those pieces of information that must be kept secret in order to prevent a grave danger to the external security of the Federal Republic of Germany. Netzpolitik.org published information about the internal structure and plans of Germany's domestic intelligence service, which is highly unlikely to affect Germany's external security.
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Relevant legal analysis (in German, by a lawyer): http://www.internet-law.de/2015/07/ist-das-landesverrat.html
The key point is that state secrets can only be those pieces of information that must be kept secret in order to prevent a grave danger to the external security of the Federal Republic of Germany. Netzpolitik.org published information about the internal structure and plans of Germany's domestic intelligence service, which is highly unlikely to affect Germany's external security.