When the ship comes you cant see it. so the only way you know the ship has arrived is to click "cherry" and then see if she say you can aboard the ship.
You dont have to take the ship, talking to the NPC will let you skip the boat ride. However yes, the boat ship itself doesnt show up- and its known. You can keep an eye on the times if you want to actually take the boat ride. The ship leaves every 15 minutes and technically takes 10 minutes to arrive.
