1) Only some weapons (like missiles) use ordnance. Such weapons generally store a small amount, but you usually want a few ordnance bays around for longer missions.
2) Cargo is one of the remaining sticking points in the UI.
4) Missiles can not miss. Perhaps it is the evasion value of the missile itself, used when PDC target it?
5) No, but people allegedly wanted "infinite" tech levels, so there are way more levels than there need to be in many cases.