Target ID
ROE and modern sensors enable BVR ID. The F35 in all its marks will have multiple ID sensors and a link system meaning it will be able to engage bandits autonomously under most ROE. Luckily for our modern fighter pilots (including F18s), Vis ID is a very restrictive part of history in most of the likely scenarios.
The "how many shipboard aircraft is right?" question relates to politics and money. How much are we prepared to pay and how important is it politically? That may be another debate in a different thread? I am new here.
The RAN currently has no long or medium range air defence capability so the fleet should not go outside the combat radius of the fighters at its nearest friendly fighter base. Or at the least it must operate with a friendly Navy who has some fighter cover, decent ship based radars and area defence missiles. NB: the RAN does not even have an Air Warfare Destroyer at present. To summarise, right now we have an inshore Navy being asked to act like a blue water fleet. We actually value our Navy personnel so little that we send them out without top cover. With the best will in the world, close in weapon systems and poorly supported (in a radar sense) FFG launched Standard missiles will not protect our people from a determined airborne attack.
Definitely, the enhancement of the RAAF F35 fleet with a sensible number of F35Bs will be beneficial overall. The ability to embark a small squadron of 6-8 fighters makes a fleet infinitely more secure/survivable, and makes it several magnitudes more threatening to our potential aggressors. The truth is, Tindal and Willy based fighters are for defence and the primary mission of the Navy has always been to take the fight forwards where the fighters will find it hard to go.
AEW and AAR are all good. They are a part of the picture to bring land based assets forward and when employed as such they will certainly enhance the battle space around the fleet.
You can actually man a 24 hour 2 over 2 airborne CAP using 6-8 ship based aircraft. Many smaller navies do it/have done it. The question needing to be answered is how many land based fighters, tankers and AEW would be needed to man a 24 hour CAP ahead of the fleet? In my experience it is something more than everything the RAAF has, and remember fleet air protection comes way down the list of priorities in the RAAF directive. Without air cover our fleet may well be targets. With air cover they are a very formidable offensive weapon.