Novaliths are entirely countered by building starbases with axillary government or equivalent upgrades. They prevent the planet from being lost to bombardment, including Novaliths.
They don't prevent you from losing your population and infrastructure, though. I like how shield generators (TEC only) mitigate some of the damage, but the advent are screwed.
I recently had an issue where my AI ally had his main fleet stationed at my planet, because it's the only planet accessible from a phase lane to the star (it's a huge 2-star map, where me and my allies had taken over all the planets in our solar system and the enemy completely controlled the other solar system). It makes sense that he'd station his fleet there because waves of enemy fleets are occasionally phasing into this system from the star's gravity well.
Well my ally just so happened to have an Akkan stationed literally right next to my planet, and the enemy was bombarding it like crazy (along with all my other planets, but hey). In anticipation of losing my planet, I also had a Progenitor with autocast Colonize parked right next to the planet, with its forward arc facing directly toward the planet.
Well as expected, the novaliths came at a rate faster than my infrastructure could rebuild, so I lost the colony after it survived about 8 volleys. And despite manually ordering my progenitor to colonize the planet, somehow the ally's Akkan snuck in there faster and stole my own planet from me. I about declared war on him right then and there, as we both had a titan in the gravity well along with several cap ships and my maxed starbase would have probably tipped the balance in my favor... but then I realized I'd lose 4 diplomatic Pacts plus all the trade with that guy if I declared war on him. Plus I'd have to purge my own solar system of an enemy before I could start attacking the idiots spamming me with novaliths.
Still, it put a very bad taste in my mouth and I saved and exited the game to come post here. I'm currently very tempted to flat-out delete the novalith's entity file and be done with it. It's gay and completely ruins the point of having a fleet. It's Supreme Commander and the nuke wars all over again.
I bought this game because I wanted to see giant space ships shoot each other with lasers, NOT to see some stupid-looking space station spam population-killing bombs at my planets from the other side of the galaxy. And the Advent Deliverance engine isn't even a viable counter, because I shot EIGHT simultaneous Deliverance engine bombs all at the exact same moment at the same enemy planet and nothing happened. N-O-T-H-I-N-G. It's like I didn't even fire at it. If you're going to make a gay TEC superweapon, at least make the Advent superweapon equally gay. Sheesh.