Barrel length does not affect accuracy. If you use iron sights the length of the sighting radius has an effect on accuracy.
If you use light loads the difference in FPS would be negligible the heavier loads will show a bigger difference. With magnum load and black powder it could make a noticeable difference.
Pyrodex is a relatively slow burning powder so with a heavy load and a light bullet the difference will be noticeable at about 100 gr.
If you only use the gun for 100 yds and under you will not see much difference once you start shooting 200 yds it will show up.