I would argue that if you dont want to have these techniques made open in court, then dont use these techniques to pursue someone who will have charges brought up in court. National security investigation techniques implies that this was a case of national security. Seems a bit petty to use these resources to defend disney, pop music, and porn.
I'd love to see a judge say: "Look GCSB, if you can show that Dotcom was a known national security threat to NZ while you were doing this, we can talk about keeping some things off the table. But if you can't, then you weren't doing 'national security' operations and no 'national security' techniques should have been used, and I want to see every single bit that's even tangentially related to this and enter it into the public record."