Fascinating, can you fix the water pressure in my neighborhood? Because I live on earth, where a gas or liquid filling vacuum or area of lower pressure decreases in pressure until it completely fills the area and meets itself trying to come back out.
Your assumption is that air molecules would all be traveling perfectly straight down the opening and not interacting with each other. This interaction is what prevents the rising water scenario you describe.
However, this could be even more distributed by putting an inverted cone muzzle on the tube, when the small end opened the entering air would decrease even more greatly.
As any method is just a delaying action anyway though, why not do as I suggested and allow pressure into the tubes terminus from its sides just before vessel passage. I'm sure you would agree that this could be done gradually, as air cannot possibly reach equilibrium within seconds, let alone the thousands of second we're talking about over a length of several miles.
Because I live on earth, where a gas or liquid filling vacuum or area of lower pressure decreases in pressure until it completely fills the area and meets itself trying to come back out. Oh, okay. Well, here on earth, let's say the atmosphere is about 30 km thick. Based on that, and the earth having a diameter of 12,750 km, the volume of the atmosphere is approximately 15,393,367,321,000,000,000 m3. When you open your vacuum tube, you're increasing the volume of the atmosphere by the volume of the tube, which, at 160,000 meters long, and let's say 20 meters wide, is a volume of 50,265,482 m3. Finally, since our opening is on top of Mt. Everest, the air up there will average around 228 mm Hg, or about 0.3 atmospheres.
Now you've got all the info you need to plug into P1V1 = P2V2, so why don't you solve for P2 and get back to me with the Earth's newly decreased air pressure, eh?