Can the seals and penguins swim into the acrylic cylinder and then up through the top or does the cylinder act as a type of "blow-hole" and then the animals have to swim back down beneath the floor again? It is difficult to discern the depth of the water due to the shadows in the room, but it does appear that the cylinder is only about a third full of water. Correct?
You're right, it's more of a breathing hole. The cylinder is actually full of water (the line a third of the way up is the refracted image of the floor), and it seems to open up onto a platform.
You can see it a bit more easily at the back of this photo:
