When exporting pdfs from illustrator there is a check box which says ‘preserve illustrator editing capabilities’ this must be unchecked when producing pdfs.
As the pdf goes through our system it reveals and flattens everything, hidden or not, within the file. If they uncheck the ‘preserve illustrator editing capabilities’ this will strip away everything in the file except the visible content.
If you have any questions on this, then please get in touch via live chat.