It is a widely accepted fact that Aramon Trebuchets are broken, thus being discouraged in most games. However, the poor sea treb is always gets lumped with its more notorious older brother, as if it was as powerful.
It's more the other units that get paired with trebs that make it so imbalanced. Acolytes, Titans, Gates, Strongholds, Mage Archers etc. There is no such equivalent on water however, making Sea Trebs a lot easier to kill.
Depending on the match up, Trebuchets on the sea should be allowed IMO.
Aramon vs Sea Treb: Prohibiting both trebs here makes sense. Its very difficult from either to kill eachothers trebuchets with anything else but trebuchets.
Taros vs Sea Treb: Difficult but not impossible
Zhon vs Sea Treb There is no excuse here. You have rocs + swamp beasts and Drakes + Gryphons.
Creon vs Sea Treb Neo Dragons and Ironclads, and both have enough hit points to easily survive a wave. Shouldn't be too difficult.