Same principle. If you already have some shortcuts created for OmniGraffle (Pro), select it in the relevant part of sys prefs>keyboard and mouse, click the + and for the Menu title input the title of the nested menu item, in this case:
PDF
Choose your keyboard shortcut (n.b. this gets trickier the more you add, and I strongly advise you to look and see what is already there under each menu in OmniGraffle - and in your Services menu too - to make sure that you aren't creating a conflict with your Services or removing the shortcut from a different entry).
Anyway, here's what you end up with:
