Currently Canviz renders what Graphviz' xdot file tells it to render. So if you have a gv file specifying that a node is invis, and you feed that gv file to Graphviz and ask it to produce an xdot file, it will render correctly.
Interactively changing aspects of the graph and re-drawing it on the client side is interesting and desirable, but I'm not sure how much of that, if any, is done in Canviz today. The intended way for this to happen is that you would programmatically alter the aspects of the entity objects and then re-render the graph.