Not an in-joke as the Soviet Union still existed when The Naked Now was produced.
But we could treat it as one.
I'm perfectly comfortable with the idea of Trek being an alternate reality where the Soviet Union simply didn't cease to exist.
The problem with that is that the dissolution of the Union in 1991 is a canonical fact, from VOY "Future's End".
Of course, we may speculate that the Union and its intelligence arm KGB were later reinstated, which is why Tom Paris fails to remember that there was no USSR as of 1996.