Lemme see if I understand your question.....

You leave Port A in State A in your boat. You enter offshore waters where State jurisdiction no longer applies (past 3 miles). You start fishing. You catch fish. You either release all of them, or you eat all you catch. The point being, you retain none of them. At some point, you return to land in State B in Port B with no fish in your possession. You're asking whether you need a fishing license during the time you're fishing/catching/eating in offshore waters. Correct?

My guess is yes, but I also realize there won't be anyone out there to enforce the requirement. It's outside the jurisdiction of either State A or State B, and the Feds aren't likely to care since you have no fish in your possession, except what's on your dinner plate. And the Feds have bigger fish to fry..... Literally.