Rather than an in-joke, I saw this more as Kyon making a connection to the common phenomenon of television networks censor bleeping out inappropriate words, most commonly with that 1000 Hz tone sound.
Television programs can also use euphemisms to censor content—for example, in the Breaking Bad episode of Mythbusters, they used "special sauce" to refer to a key chemical ingredient that they didn't want audience members knowing. I guess Kyon observed that the way Asahina uses "classified information" is similar to how TV networks censor certain things.
The anime and the written material don't seem particularly different in their presentation of this scene. For comparison:
Novel ("Endless Eight" chapter of The Rampage of Haruhi Suzumiya):
I should mention that Asahina at least tried to explain. To the accompaniment of intermittent sobs.
"Sniff, um...I normally use <classified information> to contact the future...sniff. But after a week without <classified information>, I was starting to wonder if something was wrong. And then <classified information>... I was so surprised that I tried to <classified information> in a rush, but there wasn't any <classified information>...sob. Hic. What do I do...?"
I have no idea what you should do, but does that <classified information> work like some kind of censor?
Anime (episode 13):
You've gotta watch what you say on television, eh... This question reminded me of Kaguya-sama episode 4.