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I checked briefly with one of the engineers: local notifications can update the badge, but their memory was that the API is optimized around the "show me how many times this app has pestered me" use case, which is a simpler one than the way OmniFocus uses the badge.

Our badge represents the sum of some combination of overdue, due soon, and flagged items, depending on the settings you choose.

Additionally, if the app hasn't been launched in a while, we haven't synced, either. At that point, the local alerts being fired may be based on stale data; they doesn't incorporate changes you made on other devices.

Push would has the advantage there, but then you have to pass a whole lot of personal data through a server that we run...