Multi-boxing is something that makes significant aspects of the game pay-to-win because it allows a single player the ability to multiply their contribution of various BGS mechanisms, as well as get cheaper rebuy and other benefits from multi-crew.
I certainly think it should be prohibited, but I don't expect it to be easy to catch people doing it.
Edit: regarding technical hurdles, there are essentially none of any significance. As long as you have a about ~4GiB of memory per client, you can run as many as you care to from the same physical system (virtualization helps, but is hardly required), not that the issue is running them from the same physical system, it's any mechanism by which a single player has more than one CMDR active and under their command concurrently.