Yes, AI saves hidden layers to PDF, even if you say that you don't want the result to be editable by AI, and even if you are saving to a PDF file format that doesn't support layers. This is a little annoying, but there is a workaround (without creating multiple AI files). Make hidden layers "Templates" as well (an option in the "Layers" palette). Then they will not be saved. Note, however, that you need to switch back if you ever want to show and save the hidden layer, because even if it is showing, a template layer will not be saved.