I have done some testing to figure out what is going on with the weird amount of deck pens. It seems to have something to do with the ballistics of shells being bugged. The game seems to have standardized the angles for incoming shells for all guns. Here are the guns that I tested so far. Will test more later.(I am testing guns with 1940s tech level)
16in mark 3s 15in mark 4
20km+ = 89 degrees 20km+=72-89 degrees
20km = 75 degrees 20km= 70 degrees
15km = 54 degrees 15km = 49 degrees
10km = 34 degrees 10km = 31 degrees
5km = 16 degrees 5km = 15 degrees
1km = 3 degrees 1km= 3 degrees
To make sure I wasn't crazy, I also tested 3 different 16 in guns and made sure each gun had a different shell velocity from one another:
Gun 1 Gun2 Gun3
842m/s 730m/s 641m/s
20km+ = 89 degrees 20km+ = 89 degrees 20km+ = 89 degrees
20km = 75 degrees 20km = 75 degrees 20km = 75 degrees
15km = 54 degrees 15km = 54 degrees 15km = 54 degrees
10km = 34 degrees 10km = 34 degrees 10km = 34 degrees
5km = 16 degrees 5km = 16 degrees 5km = 16 degrees
1km = 3 degrees 1km = 3 degrees 1km = 3 degrees
I'm sure this confirms that something is going on here.
PS: The game does tell you how steep a shell will impact a ship. The screenshot below shows how to find this stat. In the screenshot, the shell will impact the ship at a 54 degrees which equates to about a 13% chance to hit the belt and a 87% chance to hit the deck.