Wouldn't Size 9 torpedoes in fighters be considered "game breaking" when the Retaliator already has S9 and the Polaris capital ship has S10?

The Eclipse was designed from the start to carry S9's, the tradeoff is it doesn't carry much else and is neither very tough, nor agile. It's not designed to be a dogfighter, but rather a very specialized bomber that wants to approach a target silently, fire its payload, and leave. The Eclipse carries three size 9 torpedoes, and two size 2 ballistic gatling weapons. These larger torpedoes take a while to lock on to smaller ships, and combined with its relative lack of agility, that will mean the Eclipse will have a tricky time trying to use them in a dogfight.