Forgive me if my comment seems ignorant, as I've had experience with MPI and threaded code, but not professionally. I also do not provide any numbers or profiles.
I would think message passing in terms of MPI is acceptable, because "the cost of copying" is insignificant to "the cost of network latency." When you have very little overhead (multiple threads performing atomic operations on shared memory), then "the cost of copying" becomes relatively significant. And if you want to target JS given existing legacy C++ code that probably won't be rewritten, well then the JS execution environment will have to be the one to bend.
Which existing C++ code are you referring to? It seems like a bad idea to compromise the soundness of Javascript to do whatever it is you are talking about doing. I don't think that legacy C++ code is something that should be causing anything to bend.
I would think message passing in terms of MPI is acceptable, because "the cost of copying" is insignificant to "the cost of network latency." When you have very little overhead (multiple threads performing atomic operations on shared memory), then "the cost of copying" becomes relatively significant. And if you want to target JS given existing legacy C++ code that probably won't be rewritten, well then the JS execution environment will have to be the one to bend.