This problem is about a rather complicated thing, so I do not know the answers for sure.
Any solid body will produce sound if you tap it. But the cup is hollow and the air inside resonates to some of the vibrations of the wall and standing waves can form. You have a stronger and less noise-like sound if there are standing waves.
The fundamental mode of a cylinder open at both ends is a half-wave, as there are anti-nodes at both ends and a node in the middle.
If one end is closed and the other is open, the fundamental mode is a quarter wave. The length of the cylinder is the same, so which frequency is higher?
But it is possible that this frequency is too low, and the generating vibration does not contain it. Then it is possible that the standing wave has two nodes and two anti-nodes, that is the length of the cylinder is equal to 3/4 wavelength.
When I tried it with my cup it sounded definitely deeper when the opening of the cup touched the water surface, so I got the fundamental mode, I guess.
I understand the third question that the whole cup is under water. but I do not know the answer. When trying with a metal cup, the sound was deeper. With glass, it was the same as in case when only the opening was under the water.
ehild