The battle inside the Ghost Ship can be skipped simply by performing Leaf Pumps and grabbing the ledge on the other side.
Along with receiving Triforce Chart #4, the Ghost Ship is also used in speedruns to farm the necessary 3184 rupees needed to decipher all of the Triforce Charts with Tingle. This can be done by repeatedly entering the Ghost Ship, collecting approximately 310 rupees in the pots, and then save warping.
By voiding out in the Ghost Ship, you can respawn the pots that hold the rupees near the chest without having to savewarp and sail back in. This also means you won't have to worry about the day/night cycle when farming the Ghost Ship for rupees. To start, target the chest from the front until your angle locks onto it (keep holding L for the rest of the trick). Move backward until you're past the door frame and then left so that you're almost at the edge of the platform (pull back the camera with the c-stick so keep the camera's position relative to link the same). Run forward so that link stands on the edge of the platform next to the door frame, and against the wall. Now place a bomb, back up a little bit so you don't grab the bomb, sidehop, and then pull out the leaf and hold right on the controller, so that link flies back to the ledge. Cancel the leaf to grab the ledge and then hold down to ledge clip right. If done correctly, Link will go through the wall and void out, which will spawn you back at the entrance of the ghost ship. Magic is also tight while doing this trick about 7 times in the current route, so be cautious of it.
Much harder, but it is also possible to clip OoB to reload the area using a L-Slide Clip.
The Ghost Ship only appears at night, so manipulating the Day/Night cycle is crucial in a speedrun in order to skip having to obtain the Song of Passsing or needing to wait for the Ghost Ship to appear. Click here to see how the day/night cycle works in Wind Waker.