There is renewed activity in embind, so if it's useful, I think it's safe to use.
In general, the webidl binder does much less than embind - it just lets you write IDL that is used to wrap compiled C++ classes for use from JS. And it supports basic types but not sophisticated c++ things like smart pointers and std::strings etc. If the webidl binder is enough for you, then I recommend using it, since it's simpler and has much less runtime overhead than embind - that's why it's used for box2d.js and ammo.js.