This has been a significant limitation of Simulink for some time now. We've put together some custom blocks to stream data to disk during the simulation to get around this limitation. First iteration used an m-file sfunction to use matlab code to write binary files, however the run time performance of that was unacceptable. We ended up writing an inline c sfunction to accomplish this, which had much better performance. I've also seen other similar implementations using embedded matlab w/ inline c code as well.