I was a little surprised by this too. The "report" was about the "Bullshit Ceiling" (along the lines of the debt ceiling). This is only speculation, but I'd guess that they really wanted to run the segment, but decided it would sound all wrong if every utterance of "BS" was bleeped, given that there were so many of them. So (further speculating), Comedy Central's Standards and Practices (or whatever the cable version would be) gave them special dispensation.
I don't think it was that the "S" word '"got through a few times" on Conan , because I remember hearing it a lot. I think TBS decided not to censor it in the early months of the show, then changed their mind. In general, cable has been inconsistent about the "S" word, and a few other supposed profanities, like the use of the hyphenated word for "BJ."
Since cable is not regulated to the FCC, they can experiment with varying levels of censorship without worrying about those big fines.
Remember that the episode of South Park, in which the "S" word is uttered something like 200 times (with a counter at the bottom of the screen) first aired on Comedy Central about 8 or 10 years ago.
