The rarer the knife and better the condition the more it effects value. Collectors pay the best prices(IMO) and they prefer good condition and full packages, if possible . A user isn't going to loose much if any, but if you put 2 identical users side by side and one has the full packaging, I would take the one with the full packaging.
Of course each transaction is unique and you may be selling to someone interested in a knife for a user and doesn't care about a box, but overall it does have a diminished value.