I only had one synthetic pop (three Awoken from Limbo, two destroyed in the events that build up to the contingency getting announced, never bothered with any others) so...that wouldn't do much in that case. Even if I had all three of them, they weren't exactly on what you might call a major colony. I thought you meant actual combat bonuses, like that their fleets get smaller or something.
I believe they did have a titan in their fleet, though I'm not looking atm and don't recall for sure.
I think that was the other poster that talked about those bonuses for defeating the hubs, but I decided to be less lazy and look at the wiki...
https://stellaris.paradoxwikis.com/Crisis#The_Ghost_Signal
It appears that since their ships spawn from those hubs, destroying them helps; although the remaining hubs appear to spawn new ships more frequently.
Another rather important detail I forgot to include is to not bother taking on any of their ships outside of the hub/machine world unless they are causing a problem for you or your allies. They generally are pretty slow to migrate to new systems giving you a bit of time to focus on taking down their hubs. I guess this is especially important in 2.2 with Alloys being more precious, so no point wasting ships on those fleets unless it poses a genuine threat, since taking out all the hubs will accomplish the same.
I actually feel woefully under-qualified to really give good advice since I've only come up against them once and defeated them (barely). But by focusing on extending my fleets weapon range as far as possible (hopefully destroying a few of their big damage dealers, before they get their first shots off) and focusing on the hubs I managed to eventually prevail...although there were quite a few casualties:
I think I needed 2 or 3 100k fleets (200 ship points per fleet I think) to take on each hub without taking too many losses (don't forget to cherry pick officers with the Cautious trait for an additional +20% more range). I did however need Galactic Defender, so without this ascension point you might need to double this.
This was on a large galaxy with the default settings (except difficulty which I think was middle or commodore?), so 1.5x crisis strength...but this was in 2.1 & I didn't have Titans to contend with.
I do have the save I think, so I can check the ship configurations I used if needed, but I'll need to roll back to 2.1 which may take some time.
