As things stand currently, there is no way to eliminate amphibious aliens in the same way as land units. Amphibious sea creatures will simply retreat back into the sea, and will soon land in another spot, in the worst case the very next turn. So if you don't want to play whack-a-mole, keeping all your shore hexes under guard is the sole option. No way to be proactive in any efficient way.
Judging from discussion I've seen in different places, this is among-the-most if not the-most annoying thing in Oceania.
Solutions that I can think of:
- An MTH stratagem that can block alien land-to-sea movement into a sea hex for a turn or two, allowing encirclement and destruction of amphibious aliens that have landed.
- A weak naval/amphibious unit (hovercraft?) that even player regimes can build, mostly meant for blocking alien retreat routes.
As a separate suggestion (which wouldn't solve the specific problem, but would be neat in general), there also could be an MTH stratagem to organise an attack against creatures in a sea zone, using MTH's number of ships + combat skill against strength of the critters, with success killing some of them.