i haven't seen a difference between horizontal and vertical bobbins - i have 2 juki machines and one is horizontal and the other vertical.
the one thing i will point out is with FMQ on a frame - you really need a vertical bobbin so that you can change it without having to remove the quilt the way you would with a horizontal bobbin.
if you're just sitting and quilting i don't believe it makes a difference - it certainly didn't in the quality of my quilting.