Doves are not difficult birds to bring down. If I had to guess, I'd guess your problem was due to not centering the dove rather than some miniscule loss of velocity caused by porting. I've never seen any ballistics tests comparing ported to non-ported barrels, but the fact that ported barrels are used by many serious clays shooters would suggest that any loss of velocity is negligible. I don't like ported barrels because they are too loud.

Most folks would consider the patterning of the two guns much more important than the porting and that would depend on their chokes. You might try patterning the two guns at a distance you think you take most of your shots and compare the two. Some guns just don't like some loads, so if you pattern, you might try two or three loads as well.