Why the Pacific submarine campaign needed two commands

Was the American submarine campaign less effective because it was divided between two commands?

Not necessarily; the distance between Pearl Harbor and Australia made separate command and logistical systems operationally sensible.

Pacific distances made a single headquarters difficult to use effectively for submarines operating from both Pearl Harbor and Australia. A unified commander would still need to coordinate boats and their logistical support across those widely separated bases. Choosing where to put that headquarters would leave one operating area far from central direction. Separate commands therefore appear to have been a practical response to the geography and coordination limits of 1942.