Ship v Scallop is a bit odd, but from what I have been able to tell works out overall.
Snakes can snipe small numbers of Scallops, and support in mid-sized fights against them with proper hit and run timing.
Hunters are actually the counter against scallops, as scallops have very low DPS and are only a significant threat when balled. A comparable number of hunters will beat them very solidly.
Before regeneration and splash, a hunter can beat about 3 scallops one at a time. Including regeneration, its about 2. As numbers scale up, hunters gain an increasing advantage because of their higher speed and AoE.
The major factor to remember is that Scallops have truly terrible damage output in water.
Ducks lose to both well micro'd snakes and to hunters. They are honestly quite bad in direct combat against Ships in water, but are effective opportunists and can overwhelm unsuspecting enemies.
Boeys are, oddly enough, weak to units with crusader support (because after they bob up they are hit by a very bursty precise hit and they are unable to move to dodge). Typhoons guarding hunters will also work. Snakes can work in high numbers, but their high health and regeneration makes it to assassinate them quickly.
Archers are a bit zany, but are mostly just beaten by snakes. They have high regeneration but very low ability to deal sustained damage (because they go flying away). Mostly they are closer to a movement impediment than an immediate combat threat.
Anyway, that is what I have come to understand about the combat matchups of amph v ship (from ships perspective).
There will likely be tweaks in the coming days, but I expect this to remain mostly consistent.
