I have read that there's less drag on the quilt with a vertical bobbin, and that you can change the bobbin without taking the quilt out of the machine.
I've quilted with a Viking Lily and a Sapphire (horizontal) and a Bernina (vertical). I haven't noticed any difference in ease of quilting due to the bobbin. The Bernina does a better job for me, but the Sapphire and I never got along anyway. I don't think the Bernina is doing any better than my Lily did, though.
Janet