Shirukens can't be used even if you are holding 1 item. It requires you to have your both hands free while it says you need 1 free hand to use the item.
I don't think that's a bug so much as bad wording on the message you get when you attempt to use one while holding a weapon or a shield. Hard to accurately toss a shuriken at an enemy while using a katana or holding a buckler-or both! Not sure how OSI dealt with them.
They would be considered 2 handed weapons, so that's why you can't use them with only one hand free.