Same problem for me. I can't throw the shuriken. I can throw the standard knife (browning), which has two mode (stab / throw), but not the shuriken. I also notice that throwing this browning knife to unconscious enemies never do damage (even at point blank range, with a high skilled trooper...). Bug ?
I haven't any commando-trooper, just some with "traqueur" skill (sorry : french game ; traqueur = hunter ?) which allow use of commando weapons at level 2.