Of course baggage is scanned after it leaves the check in area.
If your bag contains live animals, suspicious items, dangerous or forbidden goods then it will be pulled aside and looked at. It's also possible that if the airline forbids carriage of any goods in your bag then it simply won't be loaded until you dispose of those items.
As for paperwork etc, I'm not even sure US Customs would allow you to transport live fish into the country (I assume you're going back to JFK)...also they would almost certainly die on the flight, either from being hurtled around a baggage system or in the freezing cold baggage hold of the plane.
If you plan on taking them into the cabin then good luck putting them inside less than 100ml of water and a plastic bag.
Either leave the fish in Turkey or look at some kind of live animal cargo transportation as they will package and transport them properly and probably assist with the paperwork too.