Yes, but NaCl provides direct access to GPU interface libraries. You can code for OpenGL directly, rather than running your graphics code through several layers of abstraction, slowing it down exponentially along the way.

There is, to some extent; hardware acceleration for canvas. But I don't expect that to be at all comparable to native OpenGL for awhile yet. JS has certainly had some significant advances in speed over the last few years, but there's only so much optimization you can do. It's still running in a VM, so there will always be that overhead.

Another important thing to consider is that the native API will always have to exist before a Javascript abstraction can. Many triple-a titles will use brand new GPU features to sell the newest line of graphics cards. That won't work if they are making a browser game and the required interface to do those things doesn't exist yet. Javascript will always be chasing the tail of native.