The duplicate weapons bug might be from "Adding" items to your inventory, instead of just editing a weapon already in your inventory to a weapon you want.
I tried to add a few apples to my inventory to test it out, and when I loaded up my modded save in BOTW, my inventory had 4 slots of apples with the amount of each apple at "0". So I think it was the "Add Item" option in the save editor. However, even though the apples were at "0", I could still eat the apples, and they would disappear from my inventory as I ate them. So the "Add Item" option didn't break the game, so thats good.
I've noticed that happens to me in the 1.1.1 version, once i updated to 1.1.2 it works properly. But at least an option to change de color for the tunics it would be awesome.