I only own the horizontal type because that is all I knew about when I got mine... don't know how long the vertical type has been around. I do think if I were to order any at this time I would most likely order the vertical.
I really don't like that 3" cutter spinning around at 12000 rpm on a router and table, miss my shaper that felt a lot safer...
I also should point out that a lot of router tables and sub-bases and mounting plates are not designed for that large of a bit. If you got the standard oak-park mounting plate for your Hitachi then it has the 1-1/2 hole...... so you will need to get the large hole one or make a sub-table top to use the horz. bits. You might also want to check if your router has any metal ears for mounting template guides that could get in the way...
If I were using the vert. bits I would make a taller fence and some sort of feather board to keep the panels vertical and against the fence.
One other small plus is price. I have a catalog sitting here and the verticals are priced at $50(US) each while the horz. are $55
I think Jerry mentioned the only down side I can think of.... and as Hickory mentioned if you were to do really big panels it might be an issue.
Now before we leave the subject if you want to make the job easy you might want to get a horizontal router table.... the sell for less then $200 here in the US.... check out:
www.mlcswoodworking.com
Ed