To sneak onto the emperor’s flagship go near the fleet with a boat and wait until it is night. Jump into the water and dive until you are near the search area. You can come up for air in areas where there is no light nearby. When you are near the emperor’s flagship save the game as it is easy to make mistakes. Dive under the emperor’s flagship to the east end of the ship and swim to the anchor:

Climb up the anchor to sneak onto the emperor’s flagship in Veni Vido Vogo in Witcher 3 Wild Hunt.

Climb up the anchor.