I know that the niche of total air-defense is already occupied by the Phalanx cruiser, but I wanted to know if that would be the only US AA ship, seeing as, on land, the US gets: Missile Defenders, Humvees (+TOW upgrade), and Avengers, and Avengers are by far the strongest in that role.

Actually, the Phalanx pretty much functions as a naval Avenger, whereas a Ticonderoga-class cruiser, with the AEGIS system, functions more as a Paladin Tank, but with SAMs instead of anti-missile equipment (to be fair, it has both, but not as much of the latter as the Paladin has).

Also, may I suggest a reference to the real-life US Navy's new LaWS system, exemplified on the destroyer USS Dewey, which functions more as an Anti-Air, Anti-Fast Attack Boat (such as suicide boats) role?

I have a link to a video demonstrating the Laser Warfare System in action against both surface vessels and UAVs.
Laser Warfare System (LaWS)

Finally, will all/most ships have a countermeasures upgrade, seeing as they have and have had missile-defenses since the Cold War (from flares+chaff to the dual-purpose Phalanx to the high-tech Millenium Gun)?

we are aware of how real life ships and naval warfare works, and we are also aware that this mod ships does not reflect them for gameplay reasons. if we're going to follow the real life ships, every ships in this mod could be anti-everything as they are (or can be) equipped with various weapons and tech mumbo-jumbo. we just don't want to litter the rosters with redundant units, as you can see the presented units so far have clear role distinction to each other.
there might be another US ships with AA capabilities, but mostly reserved for subfactions. details about them will be announced when the time come.

Okay. I'll wait and see, I guess.