Will using one of these actually change the hard points of the ship? Turn it from a full fledged Warden into a full fledged Harbinger?

Yes, the kits give you the same statistics as the other ship, replacing parts where needed. (The most significant example of this is the Harbinger kit, which adds internal torpedo hardpoints by swapping the entire escape pod.) The only difference with the base ship will be the appearance: you'll see the upgraded equipment, but stylistic changes that don't impact specifications will not alter (ie, your ship won't change color or overall shape.)