If I recall correctly, at an undistorted scale, the water would be so shallow that surface tension and viscosity would dominate, so the depths are exaggerated to keep the flow realistic.

More specifically, tidal flow obeys Froude similarity, not Reynolds. Matching the model's Froude number to the real Bay's requires enough depth for gravity waves and tides to scale correctly, which the vertical exaggeration provides.

But the distortion makes the flow too efficient, so copper strips are added throughout to achieve the right frictional resistance.