The question is really whether/when browser APIs, augmented by js libraries, will overtake native APIs.
My guess: 5 years, plus however long it takes for people to stop using whatever version IE is on by then.
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.
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.