What about steering? Is the turning radius of such a ship larger compared to a standard hull form?
The skegs didn't seem to interfere with the maneuvering capabilities of the US BBs. They were very handy with their twin rudders, Iowa being able to turn in her own length. Note that Iowa's twin rudders were in the race of the inboard props, while Alaska, with a single skeg and single rudder amidships, was much less maneuverable than Iowa, even though she's considerably smaller. Also the Fletcher class DDs, with their single rudder, were notorious for turning OUTSIDE the Iowas. (Probably their worst characteristic. Most that stayed in service were fitted with a larger rudder to aid maneuverability.)
What effects can be expected from combat damage? What if the skeg is hit by a TT? It may protect the screws but won´t it generate an "additional" rudder due to plates bend into a direction? What about water entering the skeg and flooding it? What does this mean regarding the ships balance, trim, counterflooding etc.?
Any hit that can distort a prop can cause considerable damage, as the historic hits on Pennsylvania and Prince of Wales showed. I would say the skeg would minimize this, with more structure around the shaft to support it. Such a hit would still have a serious impact on the shaft alley, and leaking would still occur well into the ship. In my opinion, it would be less serious than those on Pennsylvania and Prince of Wales, and even though the skeg could ostensibly fill with water, it would have minimal effect compared to water ingressing into an engine room.
As for maneuver in a damaged state, I think you have a point, but I don't think they wouldn't have much impact. IF the rudders are intact, I think any 'rudder effect could be overcome. If the rudders are damaged as well, it could be difficult to try to overcome with 'engine only' steering.
So why don´t we see this stern layout more often?
I think there are a couple of reasons.
First, enclosing the shafts increases displacement. Historically, with nearly every ship treaty limited, (and even Yamato bumping into limits on her displacement) taking the skeg step is going to have to be paid for elsewhere. I think it is really only practical with capital ships. And the US built some very efficient capital ships and could afford to pay that displacement.
Second, the USN had requirements like no other fleet. With the expanses of the Pacific, always operating far from base, it was willing to pay that displacement for the protection and structural strength skegs impart. ( A good example of the strength is here:
http://www.navsource.org/archives/01/64b.htm
In the fourth photo up from the bottom, Wisconsin is docked at Guam. With skegs, drydocking a ship can do without special blocking to support the stern.)
The RN, MN, RM, KM and IJN never had that same mindset, where they would be crossing great expanses of ocean, far from base, fight a strong enemy fleet, take damage and have to return home.
My thoughts,
Big Rich