My college biology class was co-taught by an actual biology professor, who taught the actual science, and by a philosophy professor, who introduced us to the philosophy of science and to questions of ethics in scientific practice. On the last day of class, the philosophy professor admonished us to, "if the emperor has no clothes, say so."
Apparently, the jibe "the emperor has no clothes" refers to the supposedly brave and honorable tactic of calling a spade a spade, of speaking truth to power by pointing out what should be clear to everyone.
That's what I assumed, but then I actually read the Hans Christian Anderson story from which that retort is taken, "The Emperor's New Clothes." Apparently, a devious tailor enters town in the story and states that he has a cloth so fine that only the most noble could see it; to all others, it would be invisible. When the tailor "dresses" the Emperor in his new clothes, which of course no one can see, he is stark naked, yet neither he nor anyone else wants to admit they don't see the clothes. The Emperor goes on parade, and the spectators refuse to admit that they don't see the "clothes." Suddenly, a young kid in the crowd, who has no embarrassment about not seeing the extra fine cloth, cries out "The Emperor has no clothes!"
The story strikes me more as a parable on admitting the truth as we see it and NOT pointing out what everyone "knows" to be true. Ideally, the characters in the story should have not been so trusting of the tailor, and yet there's little reason (in view of their interactions with the tailor in the story, at least) why they should not believe him. People were afraid that they lacked the nobility of spirit to see what they thought was there. The young boy in the crowd was not afraid to admit to seeing what he didn't see. In other words, the people in the story are not to be criticized for not calling a spade a spade, but for refusing to admit they lacked the nobility of spirit necessary to see the clothes.