[Michael Bush]

>So, bees build hexagons with the apex in the vertical orientation; up and down, and flat sides on either side.

Sometimes... Here's some natural comb where it runs the other way. In my observation the first natural comb is almost always with the rows running vertically instead of horizontally.

http://bushfarms.com/images/PrimaryCombOnBlankStarterStrip.JPG
http://bushfarms.com/images/TypicalPrimaryComb.JPG

 

[Michael Bush]

>What will they do if you put them on foundation that has been turned 90° so the apex is to the right and left and the flat side is on top and bottom?

When I was experimenting with Housel Positioning, I did this many times in the center comb. The bees build it and use it just fine.