Often a game will be GPU-bound, in which case the JS, Flash and NaCl versions will all have the same bottleneck, GPU shaders (in fact for this reason more and more is done in scripting languages in game engines these days). If that is the case, you might as well use JS, since it will run in many more places than Flash or NaCl.
But again, there are situations where you are CPU bound, and in that case CPU speed does matter - you are very correct in those cases. Currently JS is indeed at a disadvantage compared to NaCl in that area, however, I believe that it will match it in time (through a combination of API additions like Intel's RiverTrail, and further improvements to JS engines like static analysis). The real question is then, will NaCl fix its problems (portability, adoption in browsers other than Chrome) before JS fixes its problem (speed). My bet is on JS.