I think only Parry Bonus from item you are using for parrying applies. I have read a lot on this topic and i never found anything that would explain Parry Bonus when carrying shield and weapon. But it seems logical to me that only Parry Bonus from shield is applied since you use a shield to parry.
And yes, it doesn't make much sense to parry with knife when you have a shield, but not all players are using shields.
I have seen a lot of my friends not use shields in fights (i know they have it). I must admit I don't understand that because it's intuitive for me to use a weapon and a shield together. I can only guess it's difficult for them to press two hotkeys in the middle of the fight when switching from 2h weapon to 1h weapon. I also had this problem so I added a macro on my keyboard. When i press hotkey 1 to equip my main weapon it automatically press 2 for a shield.