The ocean is a dynamic and very large place, so it's unlikely to have many large-scale effects unless humans overreact. I'll focus on the local, immediate effects of this saucer from a physical, biological, and chemical perspective.
Some things to consider about the location of the saucer- it's suspended in the middle of the Atlantic Ocean, almost directly above the Mid-Atlantic Ridge. We're a little bit above the equator and thus miss the strong, surface equatorial currents and instead have a slow surface velocity of 1-2 km/day. We have strong, driving trade winds from the northeast and are almost at the edge of the ITCZ.
Let's explore the physics of such an object before we start working with the ecosystem. The biggest change will be the shadow cast by such an object- given that it absorbs all light, it's going to cast a pretty big shadow. Because it's pretty close to the surface relative to the size of the object, we'll mainly have a solid umbra- total darkness. Near the edge, we'll have the penumbra, and finally we get back into normal light conditions.
However, the ship also probably has some mass- this may affect tides and will certainly affect sea height nearby, but as I don't have any idea about the density or thickness of such an object, I can't do more than mention it.
The best way to model this addition is to treat the area within the umbra as suddenly a part of the aphotic zone. This is normally the deepest portion of the ocean, where no light reaches, and is home to all of our favorite little beasties. Suddenly, the aphotic zone extends to the surface in a single location, which causes a restructuring of the local ecosystem.
Phytoplankton require sunlight to live. The sun powers photosynthesis, and without light, they'll rapidly die. It's worth noting that these creatures wouldn't simply swim outside of the shadow- they're unable to swim at all, which is why they're considered plankton (literally, "drifter"). So all the plankton in our shadow die within a day or two and deposit a huge amount of carbon onto the seafloor, but as that's a one-time event, I won't spend too much time on it. Essentially, we no longer have a primary producer in the area, but that only reinforces the deep-sea model.
Given that we have surface currents of 1-2 km/day and the saucer is about 40km wide, that's plenty of time for any poor phytoplankton pulled underneath to starve- especially the little guys.
At first, I assumed that zooplankton would be pretty happy about this event. The big change for them here is their diel vertical migration. Zooplankton feed at the surface during the nighttime when they can't be seen and eaten, and descend to the deep sea during the day. Initially, this implies that they'd suddenly have a horizontal daily migration as well, but they aren't designed for that. Plankton move easily and readily vertically in the water column because they're able to control their buoyancy, not because they're strong swimmers. Even though they would love to move in and out of the shadow at will, they simply don't have that capability.
Interestingly, the very first time your saucer appeared, it would cause this same daily vertical migration because the zooplankton would think it's nighttime- essentially emulating the effects of a solar eclipse. They'd feast voraciously, run out of food, and shortly die.
Bigger creatures, on the other hand, would be stoked. "Nekton" is a term that includes all creatures that move under their own power, and they've been given a huge present by this saucer- the ability to move between night and day at will. Normally, creatures in the ocean have very different activities during the day and night, usually as a predation/predation avoidance mechanism. Now, they're able to swim out into the sunlight, feed on clearly visible organisms, and disappear back into the shadow within a few minutes, not 12 hours.
This behavior is why fish are often found under piers, boats, or rafts of seaweed- it serves as a place to hide from predators both above and below.
Essentially wouldn't care. They're too deep in the ocean to notice the difference between day and night, so they wouldn't notice that the diurnal cycle has stopped. They aren't even affected by the sudden disappearance of the marine snow from above because particles sink much more slowly than the ocean currents in this location, so they're still being fed by carbon from the NADW.
I'm not a bird person, so there may be more helpful information about this group coming from somewhere else. We wouldn't expect to find many birds to begin with, but they may start colonizing your saucer if it doesn't have some way of keeping them off- which might be a good idea for the aliens to do anyway. Nothing can ruin the aesthetics of a mysterious levitating saucer like bird poop. If the birds were able to land on it, they'd probably be pretty excited- it's a good spot to stop for a rest if you're migrating, and there will be some interesting marine life behavior below that they may be able to capitalize on.
Now that we've killed off the phytoplankton, one might expect that we'd see $O_2$ concentrations plummet in the surface ocean. However, that would only happen for a few days or months, until all the respirers are dead as well. What would happen over 20 years is the transfer of oxygen into the water that would slowly raise the concentrations again. We can see that best on a concentration-depth profile:
$O_2$ actually increases in the deep sea because there's no longer much consuming it. This is the same thing we'd expect to happen under our alien saucer's shadow.
What your saucer has done is essentially take the normal vertical light distribution in the ocean and make it horizontal. Rather than moving from a euphotic to a disphotic to an aphotic zone by travelling vertically in the water column, the same sequence happens horizontally. This doesn't affect much on the 20-year scale because only nekton would be able to use it to any advantage. Essentially, expect the ocean to do what the ocean does best- change a little in a lot of ways.
Some thoughts, brought up by commenters and other answers
Deep sea fish are famous for living under pressure, but they don't need it to stay alive. Fish have control over the amount of gas in their swim bladders, and as long as they're given enough time to rise to the surface they won't experience barotrauma. As to whether or not deep sea creatures actually colonize the surface, I don't know- we don't have a ton of data on this phenomenon. I find it hard to imagine that over 20 years there would be no interaction, but it probably won't be a full-scale surface invasion. Deep-sea fish are pretty happy to stay in the deep sea.
A couple comments and an answer have pointed out that it's not going to be pitch black underneath. I agree with that! However, it's not just any light that's useful. Photosynthesis requires rather a large amount of direct sunlight or it simply won't operate at all. In the ocean, this boundary is the difference between the euphotic zone and the so-called "disphotic zone". This depends on the turbidity of the water, but in the open ocean is about 100m. Additionally, photosynthesis operates best with blue light- the same wavelength that is scattered best by air. If the light is coming in at an angle, a lot of the blue light is removed and no longer able to power photosynthesis. I'd argue that any area directly under the saucer is more accurately modeled by the disphotic zone.