The unmarked crate can blow up and destroy individual people.
A secretive governing process can overstep, undermining democracy or subverting constitutional rights.
If the crate blows up, generally the public will know about it.
If important calls are made without public oversight, then the public won’t know about them. This might deprive the electorate of a chance to shape those processes democratically or to go through the courts, where their rights could be defended or where they could be compensated for harms.
Fortunately, I can’t think of any examples of when secretive organizational processes have harbored abusive dynamics. Not even in more mundane organizations with far less authority, like the Boy Scouts of America. Public officials and their reports can always be trusted to do the right thing, so public oversight is never necessary.
I think we're on the same page on what's bad with secretive stuff.
Given that the opponents of your government can use the same information as the general public to determine the blind spots of your intelligence agencies, I'm not sure what to do about that, though I am hopeful that we're rapidly approaching the point where any motivated teenager can sucessfully spy on a government and at that point there's much less benefit for agencies to be secretive.
I hope.
But all that aside, my point was that conspiracy theories are often wrong even when there's an actual conspiracy in the same general area.
A secretive governing process can overstep, undermining democracy or subverting constitutional rights.
If the crate blows up, generally the public will know about it.
If important calls are made without public oversight, then the public won’t know about them. This might deprive the electorate of a chance to shape those processes democratically or to go through the courts, where their rights could be defended or where they could be compensated for harms.
Fortunately, I can’t think of any examples of when secretive organizational processes have harbored abusive dynamics. Not even in more mundane organizations with far less authority, like the Boy Scouts of America. Public officials and their reports can always be trusted to do the right thing, so public oversight is never necessary.