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I think the idea is that the project is a separate entity than it's actions. Just because all the actions are completed doesn't necessarily mean the project is complete. Rather than falsely mark projects as done, OmniFocus errs on the side of caution and requires an explicit "checking off" of the project (just in case you might want to add additional actions after others are completed).

If you don't want the project to show up in the "due count", assign your due dates to the actions instead of the project.

FWIW, I actually prefer this current behavior and it makes good sense to me once I understood the reasoning.