I have always been baffled by these security checks. Obviously tight security for boarding passengers is critical. But I have never figured out what they are trying to accomplish by checking for ID in the public areas of the airport.
On the other hand, despite what the article says, I have never found it to be a "hassle". I swear I have never waited more than 20 seconds either at the JR train exit or the automobile entrance. The check is very fast (and hence, probably pointless), and there seem to be enough officers to handle the crowds without a line forming at all.