Mr Burns said charges against four others, including Tuhoe leader Tame Iti, would be heard in February.
Iti, Emily Felicity Bailey, Te Rangikaiwhiria Kemara and Urs Peter Signer face charges of participating in an organised crime group between November 2006 and October 2007 and unlawful possession of firearms and restricted weapons including shotguns, Molotov cocktails and military-style rifles.
Defence lawyer Annette Sykes said three of the accused had been put under severe financial pressure after being forced to make payments to legal aid.
One had a debt of more than $20,000.
Ms Sykes three guns the police had taken were used by the family of one of the accused for pig hunting.
Justice Hansen said an application for costs would need to be filed.
His formal discharge of the 13 was met by clapping and cheering from the packed public gallery.
One of them, Moana Winitana, stood up and told the judge he was happy to be able to "open his mouth for the first time".
He said he was a lecturer and had lost his laptop when police raided his home. He asked if he could send a bill to Mr Burns.
"Do you have the power to take our names off the internet? Our names have been ridiculed."
Justice Hansen said he did not.
There were further legal arguments before Justice Helen Winkelmann on whether the Supreme Court's judgment should remain suppressed.
Defence lawyer Charl Hirschfeld said releasing it could affect the right to a fair trial for the four still facing charges.
If the court released copies containing blanked-out passages, there could be confusion.
Mr Burns said the Crown wanted the case dealt with as soon as possible because of the significant public interest.
Justice Winkelmann reserved her decision.
Mr Burns also said that now there were only four accused, the Crown was no longer seeking to have the charges heard by a judge alone, without a jury.
