For the long time I though that the depth level modified the darkness level in Battlescape, for example the deep water missions are automatically night missions, but after paying more attention while playing and reading Ufopaedia, it seems that the depth levels are mostly there to determine which one of the three underwater palette sets will be used, with no effect on darkness.
Of course, I could be wrong and had a streak of missions where this never came up, but in case the depth levels are purely cosmetical (outside of the occasional downed USO being too deep to recover in Geoscape), I suggest an option that allows Depth to modify darkness:
Shallow: No changes;
Medium: No changes during day, Dawn/Dusk missions always consider Night to be closer, leading to Night Missions;
Deep: Always Night Missions.
OR
Take the New Battle's Darkness Slider which has 16 Levels, and let the Depth Levels modify them:
Shallow Waters: Changes nothing;
Medium Waters: Add 4 Levels towards darkness OR Prohibits Darkness Levels lower than 4;
Deep Waters: Add 8 Levels towards darkness OR Prohibits Darkness Levels lower than 8.