Last Saturday we got an Final Salve Situation. One of the Oppenents Ships was the Ghost with a docked Phantom.

The Rules say all not destroyed remaining Ships are relevant for the Salve, but the rules also says that a docked ship is inactive "for all Purposes". So does a docked phantom count? or is the state "inactive" overwriting the "not destroyed remaining" and the phantom attack dice doesnt count for the final salve?

( sorry for bad english )

Yes, the docked Phantom does count for Final Salvo. It's not been destroyed.

I don't think the rules-as-written are super clear about this, but the spirit of the rule seems clear to me. Your docked Attack Shuttle has not been destroyed yet, so it counts for Final Salvo.