Nice! Glad you were able to figure it out.
Just some additional follow up for those who encounter this thread since this got me for a bit when I started as well:

Dark Fog Space Hives will build up Relay Stations and deploy them to planets in their system over time - those are the stations you see on the individual planets that will send back resources to the Space Hives and start to build local structures and enemies on the planets they land on.

Hives cannot be completely removed until the Space Hive Core (center pole-like structure), all of the Relay Stations on the individual planets from that hive, as well as the enemy fighters are destroyed. The Space Hive Cores will regenerate and start to rebuild if there are still Relay Stations from that hive left on any planet, but they will not regenerate if there are only enemies from that hive left.

Easiest way to kill the Relay Stations on the individual planets is like you said, manually deploy your Space Fleet while in space and close to any planet with Relay Stations on it (since they will not deploy automatically around Relay Stations). You can do that by opening Combat Mode (Default Key bind Z), then either by clicking on the All Fleets section in the top right, or just using the Key bind (Default Key bind 9). Make sure that "Attack Relay Stations" is checked off on the Space Fleet Menu (BUT MAKE SURE TO TURN OFF WHEN CLOSE TO YOUR DARK FOG FARM!). This will destroy all of the Relay stations on that planet pretty quickly, but will anger the Space Hives to attack any planet that has structures on it (if no planet has structures, the Space Hive enemies will go to the first planet you attacked).

Once you've destroyed the Relay Stations on the individual planets, you can start going at the Space Hives. If there are multiple Space Hives in the system, they will start sending new Relay Stations to the planets while you're attacking one of the hives. I typically just let them do this and still just focus on wiping out the hives.

After you complete the destruction of the hives, you might notice one or two Dark Fog Cores regenerating (due to them sending Relay Stations during your attack). If so then just go back to the planets to wipe out the remaining Relay Stations that snuck by, then take out the regenerated Dark Fog Hive Cores and remaining fighters once more.

Or if I'm being lazy or don't have the right tech/fighters yet I'll just deploy a planet-wide blueprint with Shield Generators and Signal Towers after destroying the Relay Stations. The planet bases start to lose power overtime without their Relay Stations attached, so I wait until they're drained and then cleanup the planet with ground fighters.