1. No for this specific example. Magnetic Pulse warhead specifies an attack with Magentic Pulse warheard does no damage. Cluster Hitter is overruled by that (the adding 1 is lost along with the rest of the damage, but the attack then does no damage).
2. For the SRM and LRM unit, Cluster Hitter only applies once. If the unit has an of SRM, LRM, or FLK, it adds 1 damage. Not for each of those, but if it has any of them.
In your example of medium damage of 3, SRM1/1 and LRM1/1/1, it would do 4 damage. 3 damage from medium and +1 for cluster hitter because it has SRM, LRM or FLK.
3. It does not have to use alternate ammo, it just needs to have the special abilities and make either a standard weapons attack or a special weapons attack using the ability. A standard weapons attack includes the AC, LRM, SRM, FLK if the unit has them. (Similar to Anti-Missile System. It affects the standard weapons attack of a unit with SRM or LRM even if the unit is not using SRM or LRM alternate ammo). Special attacks like NARC or artillery attack would not include the AC, LRM, SRM or FLK special abilities, even if the unit had them for its standard weapons attack.