The Daedelus, at least according to some of the RPG books I once looked at, was capable of functioning underwater as a submarine. That might explain it's odd design compared to the Prometheus. It also could be used as a transport for the destroid type mecha that can't fly. (Remember, the front of it opens up.) And, if one is preparing for an invasion, you don't neglect the ground/sea/air forces. (Not to mention the potential uses against insurgent forces that just might go against the RDF.) As to why they were attached to the SDF-1, they weren't damaged as much as the ARMDs they intended to dock with and didn't use up their store of weapons 'cause they didn't see much if any real battle.