Hi Enrico,
I believe the layers are an inherent part of the PDF structure from a file source like AC. I recall long ago looking to restrict access to the layers within the PDFs (for perceived security purposes), but did not find any practical solution, either from the source program (AutoCAD at the time), nor by using tools within an authoring version of Acrobat Pro. Looking quickly again today, I did not see anything to suggest otherwise, but others may have some insight.
An alternate method may be to essentially collapse the content by converting the layouts into image files or similar 'dumb' format prior to creating PDFs. I've not attempted it with AC, but it should work. Note: I recall the conversion also removed the horizontal structure, and so it may not be scalable as a direct PDF would be. Text may also not be searchable. Once again, these notes are from old experimentation, so there may be some newer methods available.
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