APCs are rarely deployed in deep water, and almost never in the open ocean. Tiberium, hydrophyllic as it may be, probably doesn't do well in bodies of water with less plant life to bond with. Plus the fact that the open ocean has far more potential for nasty wildlife than lakes and rivers. An alternate explanation is that the AAPCs are small enough to avoind attracting all of this dangerous attention. Kind of like how a Shah Hulud will likely ignore, say, a mouse on the surface of the sand, but even a squad of troops will piss it off enough to attack.