In the old days, that would have been nulled by the not affecting magic weapons, so if you consider a magic missile to be a magic weapon, it becomes a weapon, and so can be affected by HoS.
Nothing in the rules stops you, but it does leave a bad taste in my mouth.
@Greg DiStefano: Yes, hammer of sigmar it is, but since GW has allowed any hand weapon to represent magic weapons, e.g. mace of helstrum... when I can use a sword as a mace, what's to stop me throwing hammers?