Some more points about the movie, and in light of the prequels:
I didn't see or remember much of the latter, but I think David had been collecting all sorts of information about the Engineers, the aliens, spores, and so on, and relaying them to the company. Some works, meanwhile, reveal that the company only had some drawings of the aliens, and nothing more, which imply that they did not know anything about the aliens until the Nostromo detected the signal.
In the first movie, Ripley tells Ash that Mother had deciphered the transmission, and it looks like a warning. It's possible that it could decipher such because of information it had gathered thanks to David from the prequels. In which case, it wasn't exactly in the dark, and if it had known even the location of the derelict ship throughout, it would have made the events of the second movie irrelevant, if not illogical, because it would have visited the ship, collected the eggs (probably using drones and synths as those would not have activated the facehuggers), and even reverse-engineer any alien technology without waiting to find Ripley.