Okay, I was able to play test the new rules. Let me give an staged example to see if I am playing the new rules properly.
I have a custom WarShip attacking a Leviathan III (XTRO:Republic III, p.17) with a 10 "tube" Barracuda Capital Missile Bay. The attack LoS will pass through the Leviathan's Fore-Right hex and the Leviathan is able to defend the attack with a total of 2 AMS Bays and 2 Laser AMS Bays. At 2 Capital Damage each, the Leviathan can destroy any Capital Missile Bay with a listed damage of 8 or less. Against Capital Missile Bays with 9 or more damage, the Leviathan applies a +8 to-hit modifier. The Barracuda Bay has a DV of 20, so the +8 to-hit modifier is applied.
The attacking WarShip is making a Bearings-only (SO, p.101) attack set at Short Range. The Leviathan has Velocity, is not evading, and has active ECM. We'll assume that the Bearings-only attack's activation hex was skillfully plotted, and it finds the Leviathan at Short Range. "Artillery" attacks are the best way for a WarShip to survive the Leviathan's Capital Lasers.
1) Is the total to-hit number for this attack 14 (Gunnery +4, Side Attack +2, Barracuda -2, ECM +2 AMS +8)?
Let's say this same attacking WarShip is using a Kraken-T Capital Missile Bay with a single "tube", and the ship is undamaged. Let's assume the Kraken is skillfully guided to the Leviathan, it has fuel, doesn't use thrust on the turn of attack, and (amazingly) ends up in the Leviathan's hex.
2) Is the total to-hit number for this Kraken-T attack 10 (Special Base TN of 2 [LoS is not used], AMS +8)?
The new rule seems to make Capital Missiles more viable, while speeding up the game. Going by these numbers, a well designed ship should provide enough AMS per arc to provide 7 Capital Damage. An attacker's only real chance of damage seems to be from "overheating" the enemy ship and not allowing more AMS to fire. It looks like the Piranha and Barracuda are now the most viable missiles, and all the others have become obsolete. The special Capital Missile Critical Chance seems to not matter, since you only get one roll per bay.
Looking at the big picture, the Barracuda is hands-down the biggest winner of this new rule. It went from being useless with a DV of 2 to now having a DV of 2-40. Pulse Lasers and Sub-Capital Lasers work well for attacking ASFs, but Barracudas can now defeat ASF Squadrons' AMS. The -2 to-hit, range brackets, and +0 to-hit for Small Craft make the Barracuda the most impressive Anti-ASF weapon. It will even play well against most Large Craft, due to AMS now being to-hit focused!