After you get out of the 1st room in the ship in Neverland your party will eventually find its way into the Ship Hold. Inside you will find a save point and a green Trinity mark which brings down a ladder.
Actually this ladder will lead right into Captain Hook’s private quarters where you fight the Shadow Sora. Once you perform the trinity the ladder will unlock this wooden gate into that room. But on your first entrance this will open with a cutscene and a mini-boss battle.
After defeating the shadow Sora clone walk near the other square wooden block in the floor. A reaction command will appear to open it and you should be able to climb up/down at your own will. The Ship Hold ladder is merely a shortcut getting from the lower levels of the ship onto the upper deck. Since you can spawn at the save point in that room it provides easy-access when just landing in Neverland.