That's easier said than done, the logistical/manpower requirements to build these massive ark ships would just as big if not bigger than the crucible. With so many people on the project it'll be easy groups such as Cerberus and the shadow broker to infiltrate the project.
Well, now you're just making things up. We don't know how big these things are beyond "probably bigger than a dreadnaught", anything more specific is purely speculative. There's no basis to suggest that the requirements to build such things would be bigger than the Crucible. As I said, the workers would be sequestered, unable to interact with the outside world, and with a longer timeframe they could afford to be much more discerning in their recruitment and with the long timetable they'd need fewer people to do the necessary work.