Leaving the original idea below for future reference. In FME 2016.1, we have a right-click on a connection to allow you to "hide" it. And you can again see it faintly if you click on either its source or destination transformers. You can "Show" the hidden connection again by right clicking on the source/destination transformer to bring it back.
In combination with the new "Junctions" that are in 2016.1, we intend to yet make a right-click shortcut on a link to "replace with tunnel" which will inject 2 junctions, label them, and hide the line connecting them. That will complete the original vision. Without the most cool terminology :-(
The ability to connect two points on a workspace without a visible connection line. Each wormhole would have 2 ends to it -- you'd have a depiction of the entrance, and then elsewhere a depiction of the exit, and you could route things through them without needing a long line crossing your workspace.