OK here comes way more than anyone wants...
Buoyancy is the property that allows the boat to float on the surface. Or can be considered as an upward force exerted on an immersed or floating body by the supporting fluid (sea) – dependent on the volume of the displaced water and controlled by varying the volume of displacement.
Center of buoyancy is the center of gravity of the displaced water or the location of the upward or buoyant force.
States of buoyancy 1) positive buoyancy, 2) neutral buoyancy, and 3) negative buoyancy
Positive buoyancy exists when the weight of the body is less that the weight of an equal volume of the displaced fluid.
Neutral buoyancy exists when the weight of the body is equal to the volume of displaced fluid – this is the state at which the submarine will operate while submerged.
Negative buoyancy exists when the weight of the body is greater than the weight of an equal volume of the displaced fluid and the body sinks. In theory a submarine is designed so that when its main ballast tanks are full it is in neutral buoyancy state. So negative buoyancy is gained by flooding negative.
Now also you have to consider stability – this means that when disturbed the body should have a tendency to return to a stable state. Without getting too technical, we have to consider stability and equilibrium. There is an imaginary line with a point of intersection of a vertical line through the center of buoyancy of a floating body. When tipped the “metacenter” is moved – here comes the big part – water is shifted (weight) so one side becomes lighter, while the other side (listing) becomes heavier, thus moving the center of gravity. Under the surface the center of gravity is much lower because the ballast tanks are full. Then we consider transverse stability and longitudinal stability. (rolling and pitching)
There is much more to all of this, but the main idea is that when surfacing, you must consider that the ballast tanks are open at the bottom, so violent rolling and pitching can cause shifting water to increase the center of gravity to shift to a point that can cause the boat to roll over. Pitching too can cause the same effect – flooding ballast tanks forward or aft and the boat would sink by the bow or stern.
So it is really two main factors to ride out a storm on the surface. One is air – a storm can outlast the supply of air in the boat. Two is stability of the boat transitioning from neutral to positive buoyancy. While submerging in a storm is dangerous too. It’s just safer on the surface.
As far as sighting targets – well if you are on the surface and cannot submerge due to the storm – it’s fighting on the surface in rough seas. A surface ship (not a sub) is built to weather rough seas better. They would have a better platform for their guns.
On the Picuda (SS-382) a few times we did all we could to maintain a topside watch in storms. A couple of times we could not maintain a topside watch (lookouts would man the periscope). Even with a lifeline I was nearly wash overboard a couple of times. There would have been no way to main the deck guns in those seas.
Sorry for the long post.