Разобрался.
На стоимость влияет:

We start off with the coefficient equal to 100%
We add ESPIONAGE_CITY_POP_EACH_MOD * (CityPop - 1)
We add ESPIONAGE_CITY_TRADE_ROUTE_MOD if the city has trade routes with us
We add ESPIONAGE_CITY_RELIGION_STATE_MOD if the city has our state religion (and the enemy DOESN'T) but we don't have holy city, and ESPIONAGE_CITY_HOLY_CITY_MOD if we have the founding location
We multiply by 1 - (YourCultureInTheCity * ESPIONAGE_CULTURE_MULTIPLIER_MOD) / max(1,OwnersCulture + YourCulture)
We add the distance modifier
We subtract ESPIONAGE_EACH_TURN_UNIT_COST_DECREASE * NumOfStationaryTurns (atm capped at 50)
We add (ESPIONAGE_SPENDING_MULTIPLIER * (2 * targetPoints + ourPoints) / max(1,targetPoints + 2 * ourPoints)
If the enemy has an active counterespionage mission against us we add 100%

NOTES:

Default defines:

Где:
ESPIONAGE_CITY_POP_EACH_MOD = 0
ESPIONAGE_CITY_TRADE_ROUTE_MOD = -20
ESPIONAGE_CITY_RELIGION_STATE_MOD = -15
ESPIONAGE_CITY_HOLY_CITY_MOD = -25
ESPIONAGE_CULTURE_MULTIPLIER_MOD = 50
ESPIONAGE_SPENDING_MULTIPLIER = 100
ESPIONAGE_EACH_TURN_UNIT_COST_DECREASE = 10

И все формулы вида:
iModifier *= 100 + GC.getDefineINT("ESPIONAGE_CITY_TRADE_ROUTE_MOD");
iModifier /= 100;

Выше приведенный пример рассчитывается так:
100+12%=100*(1+0.12)=112
112-30%=112*(1-0.3)=78.4~78
78-40%=78*(1-0.4)=46.8~46

С общей религией, культурой и торговыми путями цена будет стремиться к 1.