Re: Is their an advantage to having through transom exhaust?
it can make a bit of difference even once you get somewhat above a stock smallblock and especialy if you're turning more rpms... Bond-o tagged the main issue above - the exhaust isn't the bottle neck with the stock system. even stock marine engines are running pretty close to the design limits of the combination of heads, cam, exhaust manifolds, riser, y-pipe and prop. so if you don't open up all of the places that restrict airflow through the engine, there's no gain. put decent heads, cam etc... on the engine, and now the exhaust manifold is the bottle neck. it isn't until you go to either good performance manifolds (emi, imco powerflow or stinless marine) that the rest if the exhaust becomes the bottle neck. by the way, i'm not even close to big power but am a good bit above a stock merc 350 or 454, and the stock flame arrestor is worth 200 rpms at wot. Both sets of the cheap mufflers I tried first made a difference of 400+ rpms at wot and didn't quiet it down the way I really want it to be. now we're going with better, higher volume mufflers (that have been dyno tested with well over 500 horsepower) and turn downs to redirect the sound just a little bit and it'll be right where it needs to be with only minor if any power loss.
the other issue is, how much do you really run your boat where the exhaust will make a difference in performance?
which brings me to the noise issue... I can see why folks like the wide open exhaust, but if it is set up so you can hear it in the boat, it gets annoying in a hurry - especially if you're pulling boarders or sliers, listening to music and cruising rather than running hard. and sure it can be annoying to others, but if you set it up right there's no reason it can't be fairly quietat idle and slower cruising speeds. Personally I like it with a nice rumble, but with plenty of silencer /baffle to take all of the sharp edge off it. more like a good set of performance auto mufflers (not glass packs) sound behind headers...
to the folks that don't want to hear it on the water.. If you're on a small secluded lake or river, or if you are off and fishing in the lower traffic out of the way places, then by all means I'll steer well clear and slow down if I'm going fast enough to make a lot of noise (and if we're where we have to pass close by, I'll set speed on whatever I'm driving to make the least amount of wake at a safe speed), but if you're right off the channel in one of the main areas of the sound or river inlets, or if you're up in the couple of main river areas where the high performance outboard guys are often playing, you got nothing to gripe about. At least where I'm at, there's an awful lot of water and soooo many places where there are seldom people flying by very close in loud boats. if you want quiet wind up in the many many more secluded areas. Part of it probably has to do with where I live and play the most, but that's the way I see it.
addition: if you;re pushing a drive hard, the heat from the exhaust going out the transom rather than heating the upper gearcase makes a major difference...