That's a really good question, considering the differences in an in-ground soil system versus the container mix EarthBox system. The use of cover crops is fantastic for traditional in-ground garden as this will help to return and building organic matter back to the soil system. We're primarily using (or should be using) a peat-based or coir-based container media in out EarthBoxes and the great benefits of cover crops may not be as important.
That said, I don't see any particular downside to growing a cover crop in an EarthBox, except it would require the cover crop to be grown without using a "shower cap" cover.