I don't think it's possible to use Blender's smoke or fluid domains in B4W. The way to go for fire, fluid, smoke and similar effects is particle systems, which are of course vastly inferior to the quality of Blender's photorealistic (but super-slow) pre-rendered effects. (If there was a better way, the B4W developers would not have used particles in all of their demos.)
There is one B4W demo which uses a cloth simulation and turns it into a vertex animation, but a cloth of course does not change its internal vertex array while it morphs. With Blender's fluid or smoke, every single frame is basically a totally different object with different vertex counts and connections. This is why it cannot be turned into shape keys or vertex animations, IMO.
I experimented for a short while with turning a Blender fluid simulation into something usable in B4W such as shape keys, but quickly found it to be impossible and gave up on that idea.