I’ve heard a lot of people note that it feels bad opening empty crate after empty crate. Adding more ammo, medkits, etc. or more crafting material can affect balance, so I get not necessarily wanting to do that.
What about adding “equipment parts” to the crates? Every player could just have a running count of parts, and once you reach some amount (10, 15, 20, etc) you turn them into a random item for your class. That way you won’t be opening empty crates all the time, and you feel rewarded for grinding out the missions.