That's a good point. In effect, if we look at this from the perspective of the OSI model, you're saying that whereas the application layer may contain encrypted data the lower layers may contain structured data. So the logical question that follows: is there any reason to believe aliens might use encryption all the way down to the data link layer? Maybe our neighbours are all at war and need to disguise and protect signals from each other?

Have you read ithkuil's comment? http://news.ycombinator.com/item?id=4188160