I don't know how performance compares, but from an ongoing maintenance perspective, em-dosbox is simpler: it's regular dosbox passed through the emscripten tool

I don't know how performance compares, but from an ongoing maintenance perspective, em-dosbox is simpler: it's regular dosbox passed through the emscripten toolchain. It's more likely to see performance improvements and support, and so greater longevity. It's the same reason JSMESS is emscripten MESS, instead of a collection of native JavaScript emulators.