Perhaps an 'armored cargo hold' upgrade or such?
Or perhaps a modular or compartmentalized one? That way perhaps at 50%, you start losing cargo, but it's then percentage based after that?
ie: at 50% damage, you still have 100% cargo..
But you lose 2% cargo each past?
Could be tricky for maths. Or perhaps a different way, depending on just how many different types of cargo, it splits it up.
So, if you carry a full load of one type, you could lose all of it at 50-60%..
But, if you have 50 cargo total, 10 each of 5 different things.. you only lose one 'type' of cargo every next 10% (60%, 70%, 80%, etc)
Again, could be some maths/coding issues, but give someone a reason to not just go all-in on one type of cargo all the time.
Another possibility, a separate armored-cargo bit. (perhaps smuggler hold)
So that you can have 10 (or more depending on ship) specially protected cargo. that you can choose what goes in there?