Real wooden ships can sink if they are "pushed" (as in that video) so that they are low enough that water is above their gunwales.
Real wooden ships stay afloat when occasional waves crash over them because they have
scuppers but can sink if waves crash over them so frequently that the scuppers cannot drain the water.
Real wooden ships have hatches, etc. on their decks to allow access to their interior. These are fairly waterproof when shut but crew move about. Thus the need for
bilge pumps to remove water that accumulates.
Real wooden ships float in real oceans where waves can break their backs or twist them so that their planks part and water leaks in. Thus the need for
bilge pumps to remove water that accumulates.
The largest wooden ship (not far short of the size of the hypothetical ark) ever built leaked during its lifetime and foundered with all hands.