Just like a message in a bottle at sea, a message in a logo can go completely unseen. 40 Brand Logos With Hidden Messages is a neat infographic that may wash some new info onto your shore.
Generally, the messages in logos are not hidden on purpose. There is usually just no need to be heavy handed. Having the message enhance your logo rather than having the logo be hindered by trying to shove in a reference is a tricky business. Of course, the best logos usually do this effortlessly. Whether the process to get to that final destination was effortless or not is only known to the designers though.
A lot of these “hidden messages” you may have even known already. It’s still fun to recognize something new in a logo you may have been looking at for years.