Thank the description in the bible, and St Augustine's analysis.

The NRSW translation of Gen 6:14-16 is:

14 Make yourself an ark of cypress[b] wood; make rooms in the ark, and cover it inside and out with pitch. 15 This is how you are to make it: the length of the ark three hundred cubits, its width fifty cubits, and its height thirty cubits. 16 Make a roof[c] for the ark, and finish it to a cubit above; and put the door of the ark in its side; make it with lower, second, and third decks.

So that directly answers "a door on the side."

The ark became an important feature in allegorical/metaphorical/prophetic understandings of the OT. This is largely thanks to Saint Augustine, who viewed the various features of the OT--not just the citations found in the NT--as presaging Jesus' arrival.

For even its very dimensions, in length, breadth, and height, represent the human body in which He came, as it had been foretold. For the length of the human body, from the crown of the head to the sole of the foot, is six times its breadth from side to side, and ten times its depth or thickness, measuring from back to front: that is to say, if you measure a man as he lies on his back or on his face, he is six times as long from head to foot as he is broad from side to side, and ten times as long as he is high from the ground. And therefore the ark was made 300 cubits in length, 50 in breadth, and 30 in height. And its having a door made in the side of it certainly signified the wound which was made when the side of the Crucified was pierced with the spear; for by this those who come to Him enter; for thence flowed the sacraments by which those who believe are initiated. And the fact that it was ordered to be made of squared timbers, signifies the immoveable steadiness of the life of the saints; for however you turn a cube, it still stands. And the other peculiarities of the ark's construction are signs of features of the church.

As you can tell in the passage that follows it, Augustine considers this figura of Jesus to be of great theological importance.

This wound up leading to various attempts to describe the nature of the ark (ctrl+f ark until you see the diagram).

Most famously, Hugh of St Victor wrote a series of books about the geometry of the ark. They are very difficult reads, with Mary Carruthers (Book of Memory, 294) calling them "often incoherent, impossible to graph compeltely because they shift and change." For Hugh, the arc narrowed at the top until it reached the "central cubit" (6:16, the 'roof' mentioned), which is a square edifice slapped on top of the arc. Kinda like a house.

This bulbous ark can be found in 13th-century manuscripts , and is at least that old.

That is, sadly, the best I can do -- Hugh is legitimately nearly impossible to read.

It might also be that the 'house' is trying to get around the '3 decks, but only 30 cubits' thing. Adding an extra deck 'on top' might not go against the Biblical description. But I think fundamentally it has to do with the issue of interpreting the 'roof' (which could also be read as 'window'). Boats don't have 'roofs', so something needs to be roofed on that boat...

There is another very common image of the Ark -- a rectangle, taking the 300x50x30 instruction to its logical extreme.