The greatest resource of Remnants is not their loot (although it is good), but xp and story points gained from fighting their fleets. Currently, the biggest incentive for keeping Nexus stations alive is fighting rapidly respawning fleets and getting millions of xp (and more than one story point) per fight quickly. The alternative, hunting human bounties, takes much longer and gives much less xp. I doubt taking over Nexus stations would fix that part.
With that said, it would be fun taking over Nexus if it means being able to produce AI cores and Remnant fighters and ships. Would not mind being able to take over a Derelict mothership if doing so lets the player produce Derelict drones.
What would be an incentive to destroy Nexus stations is if it drops unique loot that is impossible to get any other way, like blueprints for Remnant tech, or limited but powerful loot like more Omega weapons. Of course, the player would still want to save at least one red system to farm xp and story points for fights.
