Stores low on certain cargo has been determined a feature of ERAS and will likely stay as it is. See a recent discussion here: https://buccaneersreef.com/forums/topic/anyone-with-issues-of-stores-running-out...
The many other "hero" NPC are traveling around and they actually consume store goods too, so the scarcity is a side-effect of the 140+ hero characters roaming about...COAS had like 4 or so. MK has determined that this just forces the player to take prizes to compensate.
The scarcity of officers in taverns is also a side-effect as the population of other hero NPCs in town is accounted for during each cycle of tavern patrons. Even if those NPCs are not always physically in the tavern, I believe it does adjust down the other patrons, and regular officers wind up getting excluded. I workaround is to ask the other hero NPCs to join you, and if they accept, the you can do what you like with their ship and make them an officer instead.
The English "102 Gun" 1st Rater might be misnamed if it only has 100 guns. I will have MK review that one.
As for Rock's ship, there are several like that in the game, and it stems from the original COAS. The Dog of War, Brig Queen, Sea Wolf, and Blue Bird all have higher than allowed cannon calibers; they are just special ships, so I'm assuming that goes for Rock's ship too.