In my current game (deity), Morocco declared war on me (we're neighbors). War score starts around - 30. Fair enough, his army is better and so is his economy. I kill 4 of his units (3 musketmen and some ranged horse unique unit) and capture his 6 pop city that was closest to me. During this exchange, I lost one Knight. After city capture, score is still staying at - 30 and it only lists 2 modifiers (army might and economy).
Same game, Mayans declared war during the above mentioned war. I take their closest city, killing 10+ units and losing 3. War score went from - 10 at the start to me being positive 30. His info box lists all 3 modifiers, including the missing one from the Morocco war (the war in my favor modifier). He places out and gives me 162 gold too. Don't know why the difference is there.
I don't have an opinion on this really, but I wanted to say it for more data for how the new score system is doing.