Hi Scott,
The only mouse shortcuts I remember from older versions is the double-click to bring up the SIF parser. Is that what you mean? Cytoscape 2 had a drag and drop panel that you could use to drag elements onto the network, but I don't remember any other shortcuts. In any case, currently, yes, the only way to add nodes and edges is through the context menus. I've tried to generate interest in getting a google summer of code student to work on the drag and drop editor panel, but no taker's so far.
-- scooter