The rules for underwater combat visibility on page 117 of the DMG seem vague and do not make any mention of the benefits of darkvision. Nor do they specifically mention that the 60 foot encounter distance (which we assume is the furthest any creature can see underwater, regardless of darkvision) in clear water with bright light is due to obscurement. What it does say, in part, is
Unless the characters have light sources, use the Underwater Encounter Distance table to determine the distance at which characters underwater become aware of a possible encounter.
This leads us to believe that: IF there was a light source, (e.g., the continual flame spell cast on an object) AND the water condition was clear and dark THEN all creatures, regardless of darkvision, would be able to see out to 40 feet, albeit with perception penalties.
Here's where the question comes in:
If that continual flame were to be extinguished, what prevents a creature with 60 feet of darkvision from seeing out to 60 feet?