The only reference I heard made to Snowden was in the very last question where an audience member asks Colbert how to keep people from being afraid of the government. In his reply, Colbert asked if what Snowden did was illegal, and when the audience said yes, he essentially said one of the bravest (and most morally admirable) things Snowden could do after breaking an unjust law is to face trial and accept the resulting consequences. His position came across to me as a combination of civil disobedience and traditional stand-and-face-the-music thinking. He didn't at all come across as vitriolic of Snowden or deeply offended by Snowden's actions.
Here's the video: