I think the reason would revolve around the fact of having AI controlling everything. By only having Arks under AI surveillance, most people would be more akin at having their own lives and work depending on their own efforts. SAM seems to work better when learning from direct interface with implants, which might not be really a popular idea with everyone, even higher ups. People need to feel they have control, and not being controlled. You might imagine that some of them would not feel like Alec was a nice guy, perhaps using SAM to seize control over the entire Nexus.
But as a contingency plan, yeah, why not? That's my opinion.
