I just took a class on long-arm quilting last week, and the instructor said she prefers the seam to run top to bottom. When the quilt is loaded on a LA machine, that seam ends up running horizontally, preventing the lump that was just mentioned where the seam is. The instructor also said she doesn't like the seam opened, because that is a point of stress, and if the seam is pulled apart, the batting will show through. If the seam is pressed to one side, then you won't have the seam opening when it is stressed or pulled apart a little bit.
In the past, I have always pressed my seams open but it did make me stop and think about it.