I've have no problem with the way the deck guns are calibrated now in RUb, but of course I'm using the 10.5cm gun on the IXB, which probably makes some difference. I sank a large cargo a couple of days ago that was steaming alone in calm seas. I only had two torpedoes left and was on my way back to Lorient. It took almost all of my HE ammo and for awhile I was wondering if I was doing anything to him, but finally he keeled over and croaked. On a different patrol I finished off a T3 that I had damaged with a torpedo after she had fallen behind the convoy. It took a fair amount of ammo, but it didn't seem excessive, though I can't remember the exact number of rounds.
I would think the amount of damage would vary a lot depending on the construction of the vessel and the type of cargo it was carrying, not to mention the quality of its crew and their skill at damage control, but I know all of this is impossible to mod in the game. I used to work for Maersk-Sealand and we had some huge vessels (up to 6600 TEUs back then) and there are even bigger ones now, and even 4400 TEU ships had dead weights of as much as 65,000 metric tons (how's that for your tonnage totals!), but to be honest they didn't look like they could take much artillery fire. But then, despite their size they're probably not as "well-constructed" as they were back in the day, and the design philosophies (as a result of containerization and economies of scale) are different.
I'm not unconvinced by Beery's list of sinkings with the deck gun showing how ineffective it was, but is there any more complete list of sinkings or logs of deck gun action? I would think these examples demonstrated one extreme of deck gun effectiveness, and there are probably half a dozen other reports that would demonstrate the other extreme, but I readily admit I could be wrong.
Anyway, just some food for thought. I'm happy with the deck gun as is, except I did use CCIP's mod to change my rate of fire to 3 rounds per minute, which I felt was more reasonable for me because I have an experienced crew, I only use the deck gun to finish off cripples or strays, and I'm usually trying to squeeze my play time in, so I'm in a hurry. You can't play the vanilla SH3 game of shooting it out with escorts anymore, anyway, because with RUb your ass is grass if you try, which is as it should be.
