DR is different than hardness. The only constructs with a hardness are animated objects (at least in the DMG), using slightly different rules than DR.
Magical attacks ignore DR but not hardness. Having said that I'd have to partially agree with Merak... a magic missle spell is an instantaneous effect, so I'd say that the object's hardness would be subtracted from the total damage done by such a spell.
You wouldn't roll a serperate caster level check to defeat SR when using magic missle vs. one creature, so the same mechanic should apply here IMO.