I haven't used the application (can't on Linux), but if the graph doesn't require user interactivity, using Cairo or some other software renderer (e.g. http://www.antigrain.com/) to just render the graph into a bitmap, would do the job faster and with less resource usage. Adding user interactivity on top of that shouldn't be a lot of work either.
Yep. They could also use some shared C/C++ bits to generate various drawing metadata ("the model") and delegate the rendering/input handling to whatever platform-specific APIs.
It may be more work, but if you're not going to build an actual native app, why bother? These apps are built as a sales point ("look, we have a Mac app!"), without the customer in mind.
It wouldn't have been as nice or expressive as Javascript though. But it also wouldn't have required hacks like stitching together a giant string to be `eval`', for example. So there's a tradeoff.