I used a longshaft 9.9 four-stroke Honda BF100 on my Zodiac C310 for a number of years...it's a beefy engine. Even with a Doel fin, it took longer to get on the plane than an equivalent short-shaft Mercury 9.9 HP two-stroke, but this could be a function of 30 lbs. more weight plus the lever action.
Once on the plane, however, I drove the Zodiac two knots faster with the Honda. I also noticed that the longer shaft, perhaps by virtue of acting a bit like a powered rudder, gave me a bit more maneuverability, tighter turns, etc.
Naturally, of course, a longer shaft increases draft. Some interesting little lagoons chipped the paint off the long-shaft's prop until I used a bit of tape to use an oar as a depth sounder...
So there are minor differences. Short shaft is a little lighter...which may or may not be an issue. Long shafts will sell better second-hand to small sailboat guys...the short shafts clear the water too easily!