RuB 1.44 adjusts the reload to more realistic times apparently (I have no idea what the actual times where so I'll take their word for it). Like wetwarev7 said if your running SHIII Commander you can adjust these reload times.
As far a not seeing any damage. I'm almost 99% sure RuB 1.44 also decrease the lethality of the rounds. Again, to realistically represent the difficulty of sinking a ship just using the deck gun. I think I read somewhere in on of the Readme's for a mod in the RuB package that it also toughens up certain parts of the ship so you don't see the whole command tower or bits like that go flying off the ship as often.
RuB 1.44 also (again I'm not 100% certain) makes it easier to use your deck gun in less than perfect weather. I guess the stock version put some strict limits on using the deck gun unless the conditions where damn near perfect.
Sorry I give you more definative answers. It's been awhile since I read the Readme for RuB 1.44.
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http://www.subsim.com/phpBB/viewtopic.php?t=37230