As others have mentioned the LHA-6 does not have a well deck as it's focus is on air operations. It would be paired with a well deck equipped LHA to allow the other ship to focus on ground ops while the America provides air support.

By the specs the F-35 should be able to carry 2 AGM-88Es on wing mounts. The current database doesn't have that as an option and some of the new doctrines being discussed can't be simulated properly without SEAD.