It’s key to note that though Marshall was the Chief Justice of the Supreme Court, at the time it was customary for justices to handle other criminal matters in districts that corresponded to their position. Because we live in the future, we can easily pull up the transcript of the testimony and Marshall’s response. It’s a complicated back and forth (abbreviated in the link; the full transcripts are even denser), but Mr. Willie (whose first name I cannot determine) has stipulated he didn’t know the cipher. One of the prosecutors asks:
He has sworn in his deposition that he did not understand the cipher of this letter. How then can his merely copying it implicate him in a crime when he does not know its contents?
Ultimately, Marshall says he’ll consider the question, and then a few days later issues a lengthy ruling. In it, he never addresses whether the secretary has stated that he knows the decoding key or keys at all; in fact, no one challenges Willie on that point. He asserts he didn’t understand the coded portion of the letter at all. Marshall doesn’t ask him either for the keys nor to decrypt it. Rather, the ruling only allowed that Willie could refuse to answer certain legitimate questions only if he swore it would incriminate him:
…if he say on oath that he cannot answer without accusing himself, he cannot be compelled to answer.
The letter itself, incidentally, was seen as less than credible, even decoded by its recipient, James Wilkson, who turned it over to Jefferson out of fear of implication. Charles F. Hobson, an expert in John Marshall, writing for the “Federal Trials and Great Debates in United States History” project, notes:
His testimony before the grand jury was undermined by indications that he had altered the famous cipher letter in ways to conceal his own relationship with Burr.
Wilkinson, who Theodore Roosevelt later labeled one of American history’s most despicable characters, was removed from his position, and later faced court martial, but was exonerated. Years after his death, evidence of his own treason became more clear.
There are still questions raised today about whether Burr intended to challenge Spain, seize a huge amount of territory, and style himself Emperor Aaron I of Mexico; tried to set up a more modest secession of territory; or wanted to secure a part of the country in which he planned to live.
The thing that’s clear is that he relied on the wrong secret keeper.
Google Books and other digitized forms of primary documents are incredibly helpful, and some are referenced above. In addition: