That has been a problem in Pacific War for its entire existence. The program heavily favors industry and supply dumps when targeting bases. Setting the bombers to the Naval Inderdiction mission will solve this, but then they won't attack anything else but ships.
I've had a little luck using Beauforts and Beaufighters, the only Allied medium bombers that can carry torpedoes. This payload option seems to make them somewhat more likely to go after shipping.
The problem in this case is that all tac/heavy bomber squadrons in the area (x2 Wellingtons, x1 B-17, x1 Hudson and x1 Beaufort) were set to Naval Interdiction. Apparently, my patrol planes failed to spot this Japanese task force during the search phase. I blame the weather. [:)] The game date was 9/27/42 --- the last week of monsoon season in India/Burma. Since version 3.2.8, monsoons actually have impact on air operations in the region. To be sure, release notes do not mention that air search is in any way affected, but I suspect it may well be.