In a nutshell, what makes a shallow water equation a shallow water equation is that the water height is not zero and it assumes no variation in the seafloor.
Note: No fluid dynamics equation will allow for a water depth of 0, as that would mean you have no fluid.
You should read the Wikipedia article on the shallow water equation.
Basically, in shallow water, the vertical velocity is ignored because the value is so small and has minor impact to the wave propagation.
To quote the section in case of modification of the source page:
The equations are derived from depth-integrating the Navier–Stokes
equations, in the case where the horizontal length scale is much
greater than the vertical length scale. Under this condition,
conservation of mass implies that the vertical velocity of the fluid
is small. It can be shown from the momentum equation that vertical
pressure gradients are nearly hydrostatic, and that horizontal
pressure gradients are due to the displacement of the pressure
surface, implying that the horizontal velocity field is constant
throughout the depth of the fluid. Vertically integrating allows the
vertical velocity to be removed from the equations. The shallow water
equations are thus derived.
While a vertical velocity term is not present in the shallow water
equations, note that this velocity is not necessarily zero. This is an
important distinction because, for example, the vertical velocity
cannot be zero when the floor changes depth, and thus if it were zero
only flat floors would be usable with the shallow water equations.
Once a solution (i.e. the horizontal velocities and free surface
displacement) has been found, the vertical velocity can be recovered
via the continuity equation.
TL;DR: In order to do what you want to do, you should be using the Boussinesq Approximation, which does not assume a flat seafloor surface.
This is a very interesting question by the way, I don't see many people try proper water simulation often.