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The PDF cropping application you are using is not removing the cropped portion from the file. It is just hiding it. Think of it this way. You have a page, within the page is a display area. The application is just making the display area smaller so that the header and footer are not shown when you view the file but they are still there.
calibre includes the ability to remove headers and footers based on regular expressions. However, I haven't gotten around to producing any GUI tools to make it easier. The process right now is a bit difficult but, it is ebook-convert in.pdf .epub --debug-input ./out_dir, look at the html produced, create a regex, convert using the --remove-header, --remove-footer and set the header and footer regexs.
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