A lot of images of the ark do not attempt to be realistic at all, in terms of scale, but only try to give a general impression; it's also fairly common to have lots of extra windows with animal heads peeking out. (This is more fun for the artist, and lets the viewer understand what is being shown.) We see versions which are just a box; a box on top of a ship's hull; or a ship that's all one piece.
- Basilica di San Marco, Venice, 13th C. - basically a box with a roof.
- Duomo di Monreale, 12th C. - box-on-a-boat. A splendid touch is the raven eating the drowned corpse of some unfortunate person - explaining why it did not return to Noah.
- The Bedford Hours, BL Add MS 18850 f.13r, 15th C. - a three-story box, with proportions resembling a church nave.
- Le Livre des hystoires du Mirouer du monde, BNF Français 328 f.4v, 15th C. - ship with a curved dome of wood, reminding me of a wooden blimp.
- BNF Français 64 f.17r, 15th C. - same idea of a domed ship, reminds me of a flying saucer.
None of these are to scale, and realism in general is not something that the artists were trying to achieve. They want to convey that this thing is Noah's ark. They also often want to show Noah himself doing things.
The Bible doesn't say emphatically that the ark is not ship-shaped; Genesis 6 gives three dimensions, but modern ships can also be summarized by their lengths, widths and heights (perhaps also draughts) with no implication that they are boxes. In favour of the box shape, it would maximize the capacity of the ark, within the specified dimensions.
I don't have any competence in maritime engineering, so I can't speak to the seaworthiness of a big wooden box, but I'd imagine at least some of the artists involved have their doubts. Including ship-like details helps to render the whole image more acceptable, especially if the ark is being shown in a stylized way already.