The separate powder bags was common at the time that the subs where designed and constructed which was the mid to late 20's.At one time all shells even smaller size ones where not fully in cased.And guns past a certain size where usually powder bag.The 6 inch guns used on the V class boats was simply a modification of a surface gun.I am fairly sure during WWII in any navy any gun over 6" had powder bags.
A site that I really like to look at and I am guessing you will as well is
http://www.navweaps.com/
here is the page for all US Navy guns
http://www.navweaps.com/Weapons/WNUS_Main.htm
Remember that the V class where designed when it was expected that submarines would stop and search a merchant remove the crew and any passengers then sink it.
No seriously they really agreed to this in treaties the UK actually tried on more than one occasion to completely ban subs.The V class where never designed to attack a warship on the surface.
Early in the war before the SJ radar was available they had to use only optics and estimate range and such.The SJ radar could actually see water splashes created by shells hitting the water it could also see land small island and such.They would use the SJ to get a good range and use the splashes to tell how short or long they where.
The small size of a sub even the larger V class made them very unstable gun platforms as a result they usually only used the guns a close ranges 2,000yds or less.
Later in the war tey actually did have "gun boats" which had two of the 5"/25 guns one bow and one stern and a gunnery computer I do not think any of these entered service in time to see much action.A few boats did patrol that had the two 5"/25 but no plotting computer for them.
Are playing any of of the Mega mods? Trigger Maru Overhauled makes the deck gun a bit less stable than stock but Real Fleet Boat wins out for having the most realistic deck gun aiming movement greatly effects accuracy you can see the boat movement in the sight and you have to wait for just the right point to fire other wise the short will be short or long.
You can probably edit some files to make the TMO deck gun be more sensitive to movement although what you would need to tweak I have no idea.