Yeah, that was interesting news. NaCl is officially removed in Unity 4.5 (which just came out). Flash will be removed in Unity 5 (if it's not already?). According to the Unity at least, asm.js + WebGL is the future.
https://unity3d.com/unity/whats-new/unity-4.5#changes https://twitter.com/UnitZeroOne/status/471355979217793024