Sign up for the
Omni Sync Service, which is free and supported by the Omni iPad apps and works with the Mac Finder, the iWork apps on the iPad, etc.
I can open OmniGraffle documents in my Dropbox in OmniGraffle on the iPad. Here's what I do:
Open Dropbox
Find the file and tap on it to open in Dropbox. See a bunch of XML.
Tap the "output" button at upper right (box with a curved arrow) and choose OmniGraffle from the resulting Open In... menu.
This does create a new document in OmniGraffle every time, and you can't save back to the Dropbox folder to my knowledge, but you should be able to open documents left in your Dropbox folder in this fashion.