The two sentences have a different meaning. For example if somebody asks: "Where is the empty box?", you can answer: "The empty box is in the kitchen!", but you cannot answer "The box in the kitchen is empty!". Though this would imply the correct whereabouts of the box, this answer would sound a bit odd since it would actually be the answer to a different question.
I was thinking the same thing and read that "in + (a noun)" refers to a general location like "Entrare in teatro costa molto" but with a sentence like this one, you would in fact use "nella cucina" because you are referring to a specific place. https://it.answers.yahoo.com/question/index?qid=20141201065540AAHteXG The discussion is in Italian, but the difference is well explained here