Ears pop with pressure?

Question

What does "even as her ears popped with pressure" mean in the following text? Does it mean her ears will be blown up almost by great pressure?

Outside, everything was dark. There was only the shadow of The Two Sisters in Exile, the dead ship that they'd been pulling since Longevity Station. It hung in space, forlorn and pathetic, like the corpse of an old woman; although Dong Huong knew that it was huge, and could have housed her entire lineage without a care.
"I see nothing," Dong Huong said, again. The ground rumbled beneath her, even as her ears popped with pressure—more laughter from The Tortoise in the Lake, even as the darkness of space focused and narrowed—became the shadow of wings, the curve on vast surfaces—the hulls of two huge ships flanking them; thin, sharp, like a stretch of endless walls—making The Tortoise in the Lake seem small and insignificant, just as much as Dong Huong herself was small and insignificant in comparison to her own ship.
A voice echoed in the ship's vast rooms, harsh and strong, tinged with the Northerners' dialect, but still as melodious as declaimed poetry.
(The Two Sisters in Exile.)

Answer 1

The phrase ears popped is pretty much idiomatic. It's defined in Macmillan, Def. 4:

if your ears pop, you feel a sudden change of pressure in them. This often happens when you are going up or down very quickly, for example in a plane.

The phrase is common in both everyday speech and literature.

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Mouths can pop open, too. When a mouth pops open, it just means the mouth opens suddenly. That would correspond with Def. 4 from this dictionary:

To open wide suddenly

Interestingly enough, your eyes can pop, too, but that might mean something different. From Def. 7 in Macmillan:

if your eyes pop, they open very wide in surprise or excitement

So, if someone's eyes pop, it might mean a sudden look of astonishment:

Vaka's mouth dropped open and his eyes popped in surprise. He scowled and shouted, "What fool eats the King's food before his very eyes?" (W. Buck)

or it might just mean that the eyelids opened suddenly:

She wasn't asleep, though. Her eyes popped open and she smiled at me. (R. Sprecht)

Answer 2

Her ears "popped" from the pressure of the loud noise of (probably the motors of?) the two ships flanking hers. This is what happens when pressure changes, like when driving down a hill fast. To prevent it, you could do this: http://en.wikipedia.org/wiki/Ear_clearing

Edit: reading the snippet again, those are spaceships. Well, they might have some problems with adapting pressure inside?