No, it doesn't say they were dead when they fell into the bunker. In fact, the contrary.
From the abstract:
> Here we show that the ‘colony’ in the bunker survived and grew thanks to an influx of workers from the source nest above the bunker
And the introduction:
> Ants which had dropped through the pipe to the bunker were not able to reach the outlet, located in the ceiling, to return to the mother nest.
And regarding your question about being able to crawl across the ceiling, probably not enough texture to grip. After all, the article indicates that there was question about whether they would even be able to crawl up the ventilation pipe:
> the only way to free the ants from the bunker would be to enable their spontaneous return migration to the maternal nest through the ventilation pipe – assuming that the rusty pipe interior is coarse enough for that
And to your point
> it's reasonable to think that the "trapped" ants are just an accumulation of worker ants that kept falling into the bunker.
Yes, and that is the premise of the study. However, a million ants didn't fall down all at once (or in a very short period), so however long they were down there they had to adapt to survive - which is what the study is about.
From the abstract:
> Here we show that the ‘colony’ in the bunker survived and grew thanks to an influx of workers from the source nest above the bunker
And the introduction:
> Ants which had dropped through the pipe to the bunker were not able to reach the outlet, located in the ceiling, to return to the mother nest.
And regarding your question about being able to crawl across the ceiling, probably not enough texture to grip. After all, the article indicates that there was question about whether they would even be able to crawl up the ventilation pipe:
> the only way to free the ants from the bunker would be to enable their spontaneous return migration to the maternal nest through the ventilation pipe – assuming that the rusty pipe interior is coarse enough for that
And to your point
> it's reasonable to think that the "trapped" ants are just an accumulation of worker ants that kept falling into the bunker.
Yes, and that is the premise of the study. However, a million ants didn't fall down all at once (or in a very short period), so however long they were down there they had to adapt to survive - which is what the study is about.