When I use the preview in macOS to crop a PDF file, the hidden content (outside of the cropped region) is still there. One can also notice this because the file size does not change.

I noticed that EPS figures can be directly opened (e.g. by vim) and I can then change the BoundingBox etc. After that, I can use TeXShop to covert the EPS file to a PDF file, and the file size is reduced. Can one do this directly to a PDF file? Does the PDF file also have a BoundingBox or something similar, which can be modified directly by vim?