The first is that you assume whatever is being kept a secret is something that doesn't favor the government, and then the government loses the case by default. This is the more reasonable option, because it mitigates the perverse incentive for the government to declare something a secret whenever it makes them look bad. But it has the obvious problem that then the government would lose some cases it should have won if the information could be published.
The second is that you assume whatever is being kept a secret is something that favors the government, and then the government wins the case by default. But that doesn't solve the problem -- you then have members of the public losing cases they should have won if the information could be published. And doing this makes the perverse incentive worse.
So why do we accept the second one instead of the first one?
When Germany, which doesn't play by the same rules, got DiDW and then Boystown, that was quite revealing on how authorities can break Tor.
Imagine the public tried to do that. Sorry, IRS/DoJ, the defendant is refusing warrants and subpoenas because it's a secret and without that you can't prosecute them.