Don't know anything about it, other than it's done. The boats I have seen with it are production cruisers, not downeasts.
Underwater Marine Exhaust Systems - Seaboard Marine
You'd think it would potentially increase back pressure but maybe a total non issue. There is such a thing as a bypass that can be used in these systems too.
For fishing I don't know, some people say engine sound attracts fish, some thinks it spooks them, maybe sometimes it does and other times it doesn't, certain fish certain times etc.. etc.. I tend to generally want the engine cut, especially when trying to pick up macks, but if things seem too quiet sitting on the hook we might startup the engine and try to give the fish something to investigate - at times I swear the generator brings them up.. On a trolling boat, or of course a stick boat, I think I would prefer the exhaust not be run this way since it would leave you no choice.
One big benefit has gotta be the exhaust layout. By running it under the water you have maximum pitch. I wonder if you may also be able to have it be much shorter, ie you can probably exit to the sides of the engine versus having to run it all the way to the transom.
Jon