10.5cm/45 SK C/32
Shell weight: 15.1kg
Firing charge: 4.08kg
Burster charge: 3.8kg
MV: 780m/s
Range: 15,175m (not that they could hit anything outside of about 1/4 of that)
8.8cm/45 SK C/35
Shell weight: 9kg
Firing charge: 2.1kg
Burster charge: Unknown, but a lot smaller than the 10.5cm
MV: 700m/s
Range: 11,950m (with same caveat as above)
http://www.navweaps.com/Weapons/WNGER_Main.htm
As you can see, the Type IX's deck gun has a heavier shell, so it carries more momentum; a larger firing charge, so it leaves the gun faster, both of which combine to give it a longer range.
The shell weighs more so it does more damage even if it doesn't explode, and a larger burster charge so it does more damage when it does explode.
But, as Jim said, none of that real-world stuff means a thing if it isn't programmed into the game. I don't know if it is or not.