Spies do not negate catapults. They simply can substitute for one of the roles of catapults - spies can be used to remove the city defenses of an enemy city for one turn (at a
cost). Catapults still fill many roles which spies simply cannot, including the critical component of a reactionary force to enemy stacks. Catapults allow one of the most cost efficient mechanisms for inflicting damage on the enemy (collateral damage) and are very important in any army, whether it is for an offensive or defensive role.
Maybe if you play Settler spies will negate catapults.

Maybe if you play Settler spies will negate catapults.