Wade in the water(s) is used it at least two ways in versions of this song. God troubling the waters, letting the Israelites through, and as a song theme during the baptizing ceremony. In other versions, the fire that will come next time is mentioned.
I doubt that there is any special "code" involved here. Of course, any word or line change in any song may be used as a code if the change is agreed upon by those who wish to give or receive a signal or pass a message. There are several versions of this song; it would be difficult to determine which one was in use in any particular area at a particular time. Even if there was a message, its form and meaning would be lost as a result of the changes made through the years.
Some people think of the Sea Islands as if they were completely cut off geographically and in time. This is simply not true. Isolation from the mainstream, yes, but the phonograph, the islands owners and their visitors, the radio after the 1920s, children going to the mainland to find work and then returning to visit, etc., would influence the way songs were preserved and would allow some new material to be added. Gullah-speaking natives of the islands were not infrequent as servants in the coastal mainland towns. We are lucky that so much was still there when the collectors became interested.