Airbases with 3 or more damage are not operational. Presumably this applies to rockets too.
I also read that they fire independently.
You are correct on both issues.
:-)
If you are attacking a lone enemy transport with a plane in let’s say SZ 1, are any of your own naval units allowed to move through SZ 1 during Combat Movement?
yes, you can ignore unescorted trns in combat movement. battles occur after combat movement.
JimmyHat is correct.
so in the same scenario, with a sub as defender, instead of the transporter (attacking with a destroyer) would the attacker still be allowed to sail through with other ships (combat move)?
Yes, as the sea zone is still not hostile.