Hi. Under new fleet building it says only 1 upgrade card per ship. Is a named ship card e.g mon Karen classed as an upgrade?

Yes.

Everything that goes on a Ship is an Upgrade card.

Technically, your Fleet Commander is also an Upgrade Card... But that one is explicitly excepted as not counting.

If a ship is hyperspacing out of a battle, does its squadrons automatically hyperspace with it or do they have to be with in a "docking" range? Also, if all of a player's ships are destroyed in a campaign battle and they still have squadrons in the play area, are the left over squadrons considered destroyed/scarred?

The advice we were given by Mr Gernes of FFG was:

Squadrons are left Behind

Squadrons that are left behind are counted as being destroyed only for the purposes of scoring

They are not scarred.