Are you sure about that, I seem to remember times when we sank the ships and captured the port and the ships spawned under the new flag.
Yes I am sure - Barring any anomalies, map bugs, famines, droughts, sunspots or rain.
If the Ships have been sunk first, prior to Port Capture, and have not respawned, and the Port is subsequently captured, the ships will respawn under the captured ports Colors.
If the Port is Captured first, and the ships HAVE NOT been sunk, then the ships
"Under Normal Circumstances" would have to be sunk, and after 10min will respawn under the captured ports colors.