I'd think that the vertical cylinder and walking beam might have saved some space on a side wheel ferry.

As for military attack, I think that's a moot point on bay ferry boat. If an enemy ship got into the bay, the ferry's superstructure is wood and the walking beam would not have made it any more vulnerable to damage.

The bay ferries with walking beams only had one cylinder, so if it stopped at top or bottom dead center, a bar had to be used to crank over the paddle wheels a bit to let steam in, or so I've read.