Security is both a reality and a feeling. The reality of security is mathematical, based on the probability of different risks and the effectiveness of different countermeasure... Security is also a feeling, based on individual psychological reactions to both the risks and the countermeasures. And the two things are different: You can be secure even though you don't feel secure, and you can feel secure even though you're not really secure."
The body scanners give the reactionary populous a reason to "feel" secure; even though the chances of a terrorist being caught by body scanners are slim. (see http://www.schneier.com/blog/archives/2010/01/german_tv_on_t...)
"Security through obscurity" would mean that there is some flaw in the security that the defenders are aware of but that they are hoping the attackers don't realize or guess at -- but in this case the flaw is pretty obvious to anyone who takes more than a superficial look at the system.
tl;dr Anything other than random is arguably worse.
Why? If every passenger is screened, how is that worse than random?