If it's illegal to send encrypted communications it will still have an impact. If the source of any unapproved encrypted transmissions could be identified there is a good chance the sender could be apprehended.
Indeed, unless the traffic/file is explicitly labeled as encrypted (protocol, file header etc.) I think there's no way to tell if a particular piece of data is encrypted or not.
More generally, the incredible stupidity in those calls for encryption bans is that the "bad guys" will abide to the law. There's a dark market for botnets etc., so why not for custom stealth encryption tools? I wouldn't be surprised if it already exists.
That's a very good point; even if it's possible to detect steganography of encrypted messages it's probably expensive to do so, especially in the torrent of digital traffic online.
I guess it will only impact law abiding citizens then.