I have a feeling that secret messages so far have only scratched the surface. The ever evolving world of advertising and social media is one that companies cannot afford to ignore, so they will be using any weapon they have at their disposal to promote their business. Messages are hidden in QR codes for anyone with a smartphone to decipher, album artwork includes them, even TV shows include them (albeit in a blink and you'll miss it kind of way), but the overriding point is that this method hooks your audience in. They are engaged. We live in a society where we are crying out for puzzles to solve because they intrigue us. Remember looking at Rubin's vase (left) for the first time and finding it fascinating? It's fair to say this is no overnight fad.
The real danger is that things will be taken too far -- too abstract and the message will be too hard to find, or even worse, the design itself will suffer. It's still important to remember that the primary image is the star, or else you've lost all sense of brand identity.
When it comes to logos, designers need to get into the mindset of making their creation a double illusion. The first priority and image your audience should see is your logo, and then hide the message within it, tweaking the design if you need to. The idea really is not to be too obvious about it.
So go out there and see what you can do. Even if you can't get hidden messages into logo designs, see where else you may be able to hide secret messages for people to find! You're giving them a puzzle book for free, and who wouldn't want that?