Ark Modules have built-in life support and do not need any agricultural/environmental population (as is the case now with orbital habitats). Therefore, the orbital population does not have to be the same species as the surface population and multiple different species can contribute from orbit.
Given that someone needs to run the life support, I think it would make more sense to have a fixed percentage for ag/env workers. Alternatively you could increase the crew requirement for the module. At the moment all 200000 colonists are serviced by 30 crew. Or you could increase the cost to represent automation like automines (although this prompts the question of why this isn't possible with ground population).
If a colony is conquered, the population in the Ark Modules will not be affected, unless the Ark itself surrenders. The Ark will be unassigned from the conquered colony. The same is true for colony transfers
Given Arks populations are separate for the purpose of planetary surrender, are they treated differently for the purpose of system claims?
On the one hand they could be doing valuable work, but on the other hand they can be relatively easily moved.
A few more questions:
Can you have troop modules on Ark Modules to help them if boarded?
How quickly can Ark Modules load population?