After I finished the first mission, a list of objects appeared, the ones I had taken (including those I've discarded) were highlighted, the rest were grayed out. Am I going to be somehow rewarded for picking up objects during a mission? It seems bizzare that replacing a filet knife with a knife would have any consequences, but the menu hints at just that.
You are not getting rewarded for picking up these items. After you complete a mission it will only say 25/25 for disguises/weapons/challenges/items found.
Disguises and guns are available in contracts mode after you pick them up.