Any unit with the Water movementtype cannot go onto shallow water in any version of AoM, however land and amphibious units can, this should be resolved as to allow water movementype units to exist in shallow water, and move through it, similarly to Age of Empires Online (made in the same engine) and older AoE Games, as otherwise it acts as an unnecessary barrier, and limits Naval unit use.
Additionally it may be wise to add a MinWaterDepth unit property to make sure the water is deep enough to allow for it to be logical.