The catapult does full damage
The catapult deals bludgeoning damage. Scarecrow, in its most recent version, has a resistance towards Bludgeoning, Piercing, and Slashing damage from Nonmagical Attacks (emphasis mine; see the monster's stat block on DnDBeyond). Catapult, however, is not an attack as the damage comes from a failed saving throw and not an attack roll, so the resistance does not apply.
You can find the change to the wording of the resistance in the Global section of the errata document here.