The embryos are more elaborately stored because humanity is terrified of anything relating to the Eugenics Wars. As for the security procedures, the station isn't expecting to be attacked by anyone since its location is secret. The human sized tubes could be used for animal testing. The embryos are still viable because of some futuristic technology. Archer shares his plan because he figures he has nothing to lose at this point. And finally, the Augments don't take any weapons because they have super strength and don't need them.