It all depends on what tool creates/exports the PDF. If the data is vector, then one tool hides parts by using paths, the other might really crop them.
I'm not 100% sure about this, but I'd say, Indesign does not crop, but uses paths. The only way I can think to rework a PDF and crop/delete parts is using Illustrator.
You can try cropping the PDF you wan tto place in Acrobat, but I don't think that actually removes the data, either, though going a couple of steps further will.
Save the cropped PDF as .eps, then distill the .eps back to PDF. Not pretty, and you lose transparency, interactivity, and layers, but it will be cropped.
@Florian – re-destilling to PDF would be one way…
1. Copy/Paste your placed PDF to a new document.
2. Make the size of the page the size of the cropped PDF.
3. Export the page to EPS and distill that to PDF (Distiller comes with Acrobat Pro).
OR: Establish a PostScript => Distiller => PDF workflow.
OR: Use a third-party tool like Axaio's PDFToolbox to do that on an exported PDF.
Message was edited by: Laubender