just from the wiki:
-the robots that are scattered in one of the rooms of Dec 13 may have a later use in the story (this is just implied not confirmed i guess)
-it seems interacting with the Shields on the nova will have an effect on the fate of Aurora (the bat girl that sells some gadgets in the town) during the Stellar Tether storyline
personally i havent taken the other options for the end of this sidemission, i always end asking Anno about what she thinks of the Nova dilemma and choose to help the crew. in fact, helping Nova is the only way to get/unlock the Gray Goo Armor so that's another effect for the list.
the mission doesnt really have much weight on what happens on Tarkus, the "wild" variant of the Gray Goo doesnt disappear or anything but you can interact with it to get charges for your Gray Goozoka. and i think you can bypass combat on the first encounter by having the Gray Goo suit during the Tarkus expedition with Azra.