I know exactly what you are talking about and very surprised this function doesn't exist and nobody has addresses it. I can easily zoom in and pan around on the ipad and iphone. There is a vertical scroll bar for the desktop version, why not a horizontal one? This should be a simple add on, similar to every other software that allows zooming.
@gazumped, the annotate command is within evernote. When you hover over the PDF, the tool bar appears up top. The annotate button is to the right of "eyeball" button and looks like "@".