(just thinking out loud..) If we assume that the size of the cell is necessary to accommodate the size of the queen, it must of necessity hang vertically because if positioned horizontally, the cell would very likely sag under its own weight in the warmth of the hive ...
Riccardo and myself were speculating on the subject.
One possible explanation is that the relatively tiny bee space would not accommodate large horizontal queen cells (compare how bent emergency cells are).
More stimulating is that vertical queen cups might elicit stigmergic behaviours. Indeed, worker cells tend to receive royal feeding and cares when turned opening down (this is like the opposite the idea of your second message).
Unfurtunately I did not find any evidence in the literature...
During the early pupation stage the queen is very delicate, perhaps the vertical orientation relieves pressure which would interfere with her development.
I would like to add this observation: in a starter colony which was housed in a "nuc" box , I have recently observed queen cells projecting horizontally from the comb. This was possible because the design of the box permitted an additional 5 - 8 mm between frames, Therefore, I would suggest that the vertical orientation of a typical queen cell may be the product of space constraints...