Does the damage rating for the creature’s attacks in core and Horror books, especially natural attacks, also include the bonus dice due to attributes or does the gm add those in?
Generally they include the stat adjustment.
Ie a poleaxe is listed as 4cd in the weapon section, but 6cd with the Berserker on page 312, and the listed brawn is 11, which provides a +2cd bonus to melees.
If you find one that seems super low, its possible it was missed. If you find creature type X is hitting…not hard enough in your game, i’d just add some damage dice.