I saw some of those comments suggesting it was funny because Shatner and Nimoy are Jewish. Only Spock knows what he was thinking when he said it, but I think it was more his attempt to make a joke (at Kirk's expense), rather than a wink to the audience.
I can understand why some people might think it's some sort of inside joke. Performers like Mel Brooks, Jack Benny, Charles Chaplin, and even the Three Stooges took pokes at Nazis in their films. But I don't think that's the case with "Patterns of Force". For the record, I am not a Zeon pig.