The only reason I would consider valid is that a vertical bobbin can be easier to change without removing the quilt. And considering how often you have to change the bobbin (depending on your pattern) that can be a considerable pain. I use a domestic machine on a quilting frame too, and would have loved a vertical bobbin access, but didn't like the machines they came in. I love my Janome, horizontal bobbin and all!

For piecing and fmq without a frame its horizontal for me.
Much easier to use and you can see if you are getting low on bobbin thread.
On a frame you have to move the machine to the side to get access to the bobbin anyway so still would prefer a top loading horizontal so I can see if the bobbin is empty without removing it first.

I FMQ on my ancient Pfaff and on my Janome and haven't noticed a difference.