I do not believe that they sink, sinking in time would be very difficult regardless.
The Amph AA is optimized vs bombers. Gnats and blastwings waste its shots badly. This should make it fairly trivial to catch an amphibious player on the shore as he exits the water, using the gunships defensively.
However, the shotgun on the scallop is fairly accurate and does a lot of damage vs gunships, and if the Bouy does hit gunships, they are slowed enough that they can no longer dodge.
Possibly an option for hitting amphs might be needed- blastwing is currently under-utilized, so that might be a good call. Im not sure this is the best mechanic though.