Jean-Claude Tremblay (an Acrobat expert and fellow PDF traveler) made this excellent comment on cropping PDFs and prepress issues. Note the link to his blog and the custom profile available there:

"You mention in your post that the information is not removed in the PDF and that’s true. It is also true that when processed by some rips the cropping will not be preserved. Fortunately, both issues can be fix with a custom Preflight profile. I have blogged about this and offer a link to download the custom profile. http://bit.ly/pdfcrop "

Thanks, Jean-Claude!!  info@proficiografik.com, http://www.proficiografik.com