Juggernaut Ship Hangar Underneath The Engineer City; Painting by Wayne Haag

I agree that the reason why they probably left it out of the film is because they maybe thought it would open a bunch of speculations amongst fans on what the city's purpose was due that there were more ships in there. Everybody would've been like "so they were planning to destroy more planets?", "do the other ships also contain black goo?", and all that sort of stuff.

I'm sure the producers wouldn't have wanted the audience to pay that much attention to the city when in reality what they want you to pay attention to, is what David was doing in that scene.

I like the way they cut this out, as if they left it in then we would have to wonder why David did not leave in one of those ships.

So having no ships in the Hanger does narrow down Plot Holes and also paint a picture that these beings on Paradise are Sacrificial Hosts or used in this way and are collected from this place from time to time by the Elders.

Based on how the one Prometheus rammed held up vs the collision, the prometheus's engine explosions, and the fall with impact on the ground, it's got to be something like a comprehensive integral spaceframe supported ceramopolymer composite hull, likely reinforced with carbon nanotubes, possibly metal-bonded on a molecular level.