Regarding the open vs. closed at A&E part. That actually isn't relevant in and of itself.
You have this cave system sitting there, full of basically stagnant water, and all of the sudden, you close the sliding hatches at A and E (you did read the sign that said the cave closes at dusk, eh?). It should be pretty clear that the pressures above and below the sliding hatches do not magically change in the instant the doors seal, right?
Okay, now let's say that only the middle of the W closes at dusk. At the moment you slide the doors at B and D closed, what happens to the pressure on either side? Well, nothing happens.
In the case of this example, whether the system is open or closed is irrelevant. The only relevant information is:
1. The pressure at a given vertical coordinate (i.e. 1 ata at point A)
2. The vertical distance between the level at that coordinate and the level of any other coordinate inside the water.
Incidentally, as the pressure above and below any water-air interface is equal (ignoring the all but immeasurably low contribution of surface tension), and as the pressure in the air in the bubble can be taken as a constant (as air has a low enough density to make the pressure changes with height negigible in a cave bubble), the pressure in any gas space can be said to be equal to the pressure in the water's surface in contact with the bubble (as determined by the height in the water column, as explained above).
(In other words, the permeability or impermeability of the surrounding rock is irrelevant to the pressure in any bubble, permanent or transient, in the cave system.)