PDFs are not first-class citizens in Evernote. If you're used to Bare Bones Yojimbo, you should realise (as I did not) that Evernote is different. In Evernote, your PDFs are incorporated into the library as an attachment to a note - not as an object in themselves.
When you want to export a PDF that's embedded in the note as a PDF file, it seems the options are limited. Using Evernote's File > Export menu item results in a proprietary XML file with the PDF attachment Base-64 encoded in the XML.
My workaround was to choose open from the contextual menu that's when right-clicking on the attachment. Once the PDF was open in Preview, I was able to Option-drag the document proxy icon (the icon in the window's title bar) to the Desktop. Unfortunately, that resulted in a file name that appears to be a hashed value, rather than the document's original filename. Anyone got a better workaround for this?
I don't want to hate on Evernote - it has a lot of great features and the sync works really well. However, as a repository for PDF files, its design does not - as far as I know - enable a round-trip into and back out of Evernote.