I think we'll only ever have that for a specific subset of JS applications, where they are written in a way that lends themselves to very aggressive JIT optimizations. Other than those, my gut feeling is that there's too many high level abstractions that JS allows to expect it to get too close to C, who's abstractions map fairly closely to hardware.
WebGL strikes me as a much more likely and more open HTML5/Native hybridized future. I don't doubt there will be other hybrid technologies but I think WebGL is the first one that's here to stay.
To clarify: I mean open as in open web here; that is to say that the WebGL GLSL code that gets compiled to run on the GPU is human readable when embedded in a website. AFAIK this is not the the case with NaCL or PNaCL.
Moving back to adoption, NaCL has only currently been adoption by Chrome and Mozilla does not seem particularly interested in changing that.
I'm not so sure about that. I thought these technologies sounded very intriguing early on, but I don't think they're going to have much impact on the future.
NaCl is weakly supported by Google, completely unsupported by other browsers and is totally architecture-dependent. It's quite possibly less portable than a normal native code app.
PNaCl is basically abandonware as far as I can tell.