Hadley's Hope was a shake n' bake colony. It was a cheap, co-funded microwave meal of an installation. Cobb and Cameron tried to make this clear by making the colony look prefabricated and simply set up on LV-426. Cobb explained that he designed the buildings as "long hexagonal, cylinder-type things that could be transported intact, lowered into place from some sort of hovercraft, and then mounted on huge concrete piers." The colony's model builder, Pat McClung, described the buildings as being built "out of giant shipping containers" The air ducts in the colony are a kind of giveaway. The colony's presence on LV-426 is no expensive, Prometheus-esque grand venture with an ulterior motive (since these plots were always secondary in the Alien films, fans have had to speculate endlessly for decades, hence 'Bishop planted the egg on the Sulaco' and other such things.)
As for the derelict's SOS, Cameron explained seismic acitivty displaced and damaged the derelict, destroying the signal apparatus. Alien covered this (unfilmed) by having Dallas simply switch it off.
The Company did not know about the Alien per se, only a signal which indicated either extraterrrestrial life or technology. The special order is likely one of, well, hundreds of orders stored within Company computers like Mother. Ash found an alien, so 937 was apt for the situation. Ridley et al spoke a lot about corporate paranoia, espionage, etc. Situations like the rerouting and an android being aboard were hinted to be secretive but not entirely unusual -- the Alien, however, was. Give this a look, it might elaborate:
https://alienseries.wordpress.com/2013/08/13/the-android/
