From what Tim told me (I haven't started digging into Vert.x 3 code yet) the module system is being replaced by jar/zip or something similar. I think instead of Vert.x resolving dependencies, the intent is to use build tools which are often much more mature than Vert.x anyways.
So, yes it's being replaced, but by something similar and more powerful/flexible. Modules and their dependencies will be self contained which, for something like Vertigo, makes it easier to distribute them across a cluster. Right now, Vertigo has to resolve, package, and zip dependencies itself in order to distribute them.
@see my long discussion with Tim about the merits of replacing the module system in the Vert.x 3 features planning post (I would link to it, but Groups acts crazy on my phone). Hint: I was opposed to it until i got a better understanding of it.