I agree with Charles, it is odd with the loot being worthless from a skull chest and a pouch with a rare item. Actually... I find it annoying.
Disney speak
We appreciate your feedback about the new Inventory System and the Lost Weapons of El Patron. When Jolly Roger and the EITC Black Guard discovered the Lost Weapons, they split them up between their forces, which is why you can now find them by defeating enemies throughout the Caribbean. As such, only Jolly Roger and the EITC know for certain what enemies are holding onto which weapons. Your best bet is to face as many new enemies as you can in order to increase your chances of getting the weapons you have your eye on. Exploring and facing new foes is exactly what a Pirate's life is all about!
Interpretation Sarcasm Alert
Pouches, chests, skull chest and all their contents are random, it was easier and faster to write the computer code for it this way.