Yes, I'm bothered by directional prints going the wrong way and I hate it if there is a strong "stripe" in the print, like polka dots that are all lined up. I have to cut these so they line up in the patches. That's why a really look at prints before I buy them.
As far as the HSTs with directional prints, you will need to cut twice as many as you need to get the print all going the same way. The up side, is that you can make 2 quilts ;-)