Thanks for the feedback. There wasn't time in the development schedule for v2.0 to include the features you're talking about, but there are a few ways to achieve these goals:
You can copy either the whole diagram, the current selection or the currently visible area onto the clipboard: select Copy from the toolbar or from the Edit menu. You can then Paste this into a graphics-compatible application with print capabilities. During the beta, it was recommended by one of our users that Excel is an excellent choice for this task, since it handles printing of such large areas very well.
To chose the print area, you could arrange the display so that the visible area contains only that which you wish to print, just by panning and zooming around the diagram, and temporarily hiding any objects you wish to omit. After pasting into an application such as Excel you can resize the image to the size you want - since it's a vector based image it should scale well in applications which support the vector format we export (EMF or enhanced metafile format).
To export to PDF, repeat the same process but chose as your destination an application which directly supports PDF export. There are a number of them out there (such as popular third party office applications). Alternatively, export the diagram as EMF and use a third party EMF to PDF converter; again there are a number of them available over the net.
Apologies for the fact that this feature isn't in Dependency Tracker. It will be considered as and when we're planning the next major release.