You should be able to observe the number and strength of an enemy fleet by having a group of scouting ships equipped with telescopes or crows nest and having the group sail past the enemy city. With telescopes you can get better more detailed information about the enemy city and fleet.
With the new scouting aspect spies usefulness will drop so they would need rebalancing. New uses could be to steal funds from the city and slow research. You should also be able to have more than one active spy in a city but the more you have the more likely they are caught and all of them are caught as well. This would increase your ability to start revolutions or other spy activities.
With new more advanced spies, cities need better defenses against these shadowy threats. This could be done by selecting where your police can stand guard. You could choose to guard either the cities defenses or cities ship yards. This specification of your police would increase the chance the spies are caught or fail to sabotage your defenses or ships but this leaves your cities with a higher percent chance of being persuaded into revolution. Also with a higher secret police strength cities have a higher chance of rebellion.