It's definitely a tough situation. I've never liked the idea of embedding fonts to be used for the main "body" font of an ebook. It takes away the choice of the reader to use their preferred font (without editing the ebook). Yet being able to reliably count on special characters showing up as the content creators intended (without asking the reader to jump through hoops) is important too.
Adobe/vendors just really needs to nut-up here and start shipping "full-featured" unicode fonts with their devices/apps. It's a big world out there... and some of it uses squiggly marks over its letters.