Presumably Sauron could've destroyed the ghosts, he was just a little distracted at that time frame, or not yet able or willing to face them directly. Like the Eagles, they can't really tackle the Sauron problem, so aren't as much of a solve as they appear.

Also the reason they only fight in the final battle I think is because that is the only battle they're bound to fight in, I'm not even sure you could use them to fight any other battle than against Sauron's armies.