The hydrosphere is an often overlooked aspect of a planet. Most people never notice it unless 1) it's zero or 2) it's 9-A. Unending sandy dunes or mile high arcologies stuffed with people are usually easy to spot.
The reason for ignoring the hydrosphere is simple: historically we Terrans don't use a lot of our ocean and what we do use is mainly the top part. Even Aquaman gets very little respect (especially from my wife for some reason) despite controlling 75% of the world. On many worlds the hydrosphere greatly surpasses the land in numbers of biomes and sheer biomass. This becomes a valuable food source on water worlds but there's no reason planets with more land wouldn't use fishing to supplement or replace their land based food sources.
Waterways can be an integral part of starports. It makes sense to have your air and space traffic move over empty ocean as much as possible on landing and takeoff when most accidents happen. If you're dealing with reaction drives (bless your heart) a water landing might be necessary to avoid patching the starport runway every day. A commando assault to capture a spaceport is a first step of many invasion plans but it might come from submarine forces and not jump troops dropping from orbit. Battle dress could probably substitute for scuba gear in shallows at least.
Water is also a prime source for the hydrogen fuel that ships use in ridiculously large amounts. Imagine a pod of whale analogs that takes interest in your Scout ship floating along. Now replace the whales with Cthulhu. Now split the difference. Cthulhu is only good if you want to start a new campaign. With new players. Who didn't talk to your old players.
A lot of material is written on uplifted dolphins, genetically altered humans and aquatic aliens. Very little attention is paid to amphibious humans (or aliens). Amphibious mammals already exist in nature so there's plenty of reference material for genetic manipulation. Creating a water breathing mammal would likely be more complicated and it would be difficult to interact with air breathers without special life support systems. A compromise could be reached with a 100% humidity breathing mixture in zero gee. But this might take a little more arranging. An amphibian would be able to exist in both worlds at least temporarily with little preparation.
Undersea civilizations could be incredibly hard to find and remain a mystery for quite a while. Aquatic aliens are likely to be very alien in outlook and a contact situation will really make the Scouts earn their pay. A well settled world with pre gravitic technology might base a lot of local shipping on waterways and even a relatively primitive race of water breathers could raise watery hell with commerce and fishing if they felt put out. This might only come after several years of observation and planning and come as a complete shock.
An ocean like the Atlantic could also be the breeding grounds of several related or separate intelligent species. While we think of an ocean as a homogeneous whole it isn't. There are pools at the bottom of saline rich r sulfide laden low oxygen water. There is the boiling heat near volcanic vents and the sunless depths under ice packs. A group of human colonist might upset a delicate political balance with their fishing and face a coalition of enemies rising from the depths.
The hydrosphere does not have to represent fresh or salt water. On a planet with a D atmosphere it could represent the surface area lying in the poisonous depths of the atmosphere. Similarly on a F atmosphere could be the heights above the breathable atmosphere. Note that breathable doesn't apply to every race equally. Two or more races could occupy a world with extreme pressure gradients at the levels they find comfortable.
Finally when you say 'sunken' many people think 'treasure'. This can be anything from sunken human shipping with mundane though valuable salvage to ancient (or Ancient) relics and outposts. After all over millennia water levels will change due to climate factors. Bases and cities might be flooded, submerged and forgotten.