As for 10.11, my experience is that Aperture runs a-ok so far, didn't encounter any problems for now and Apple is well-advised to keep it this way unless they want to piss everyone off even more.
As for Apple's photo book printing service, I don't understand what you mean by that.
Apple don't use Aperture to print the book you send to them as a file ready-to-print.
Aperture is the software that creates a file that can be printed, much like Photos probably does, after that, Apple forwards these files to their contracted printing companies around the world, depending on your location and there's no further involvement of someone sitting there fiddling with an Aperture set up to do... well what? The layout is done already.