Does counter-attacking count as that squadrons activation, or can the squadron make multiple counter-attacks, as well as attack on its own activation? Seems to make TIE Interceptors mighty powerful when coupled with Howlrunner.

It's a seperate attack that triggers whenever they are attacked. Being activated already doesn't matter nor does it cause you to become activated.

It also happens even if the ship was deatroyed in the initial attack. And as it is an attack is effected by the likes of Howlrunner and the swarm ability.

Gibbobobo is spot on. The counter attack is a free attack triggered when a squadron with Counter is attacked by another squadron; allowing them to shoot back at the squad that attacked them (even if the attack destroys them or they had already been activated). A squadron with Counter can also make a counter attack for each attack directed at them by another squadron except that a "counter attack" does NOT trigger another counter attack; only regular attacks trigger a counter attack.

The A-Wing also has the Counter trait just like the Tie Interceptor. So for example, if a Tie Interceptor attacks an A-Wing, the A-Wing gets its free counter attack against the Tie Interceptor; however, the A-Wings counter attack does not trigger the Tie Interceptors counter attack as the A-Wing's attack is not a regular attack.