You can Disable them by destroying the reserach labs.

Entrenchment provides a counter for the Novalith in the form of Auxiliary Govt. The advent culture cannon will not be devastating outside of combat (culture bonuses aren't going to help them if they have no ships there) if you have your own culture. Vasari Kotsura...well...there isn't too much you can do about that. Luckily, it won't do too much damage to things with shields. But, yes, go destroy their labs. Super Weapons are meant to be the way they are. They require a significant investment to research/build. If you spent the effort to build such a thing, then you should be rewarded with something powerful. It is too bad that the TEC Novalith is the worst off being the hardest to research and nerfed by Aux. Govt (though understandably so).

By late game income form planetary population should be fraction of your overall income.

Oh yeah

I remember those.

Beat the whole game and my brother with them ladies

It's significantly less than 2/5s. You seem to confuse Credit income with Income.  Your resoruce income is actually HUGE portion of your income, and it is not affected by this population penalty.  I had often had games where I had 10 metal per second, equivelent of 25 credits per second if I was straight up just selling the stuff.

you could build more than one novalith?

i was playing against an AI (given, this is the beta of entrenchment) and he (Vasari) had just absolutely filled his chokepoint system with mines. i mean you couldnt even see the asteroid there were mines everywhere. i sent in i think like 300 scouts (this was an early version of the beta, so the best way to get rid of mines was just scout spam) and i could not get through. so, i built 7 novaliths, targeted his planets, and fired just about simultaneously. it was some awesome fireworks, and of course, he surrendered afterwards, but yeah, smaller maps its generally hard to build enough novaliths to win the game, but bigger maps? if you back him into a corner, so hes only got a few planets, bam, thanks for playing baby.

so, back on topic, i dont think superweapons are too overpowered. yes, the novalith erases a planet... wait 60 secs and recolonise. yes, the delivernce engine shoots culture, but like someone said, without ships, its irrelevant. yes, the kostura disables structures and ships... once again, unless theres a fleet nearby to mop up, big deal. all you have to do is make sure you have the ability to wipe out enough of his labs to stop him from firing, or, just fire back at him?

one little countermeasure i have against the kostura... once you hear its been fired, move 2 or 3 planets away. if he fires at your fleet in Gravity Well A, he cant hurt your ships if they are in Gravtiy Well B or C. depending on how surrounding systems are configured, just move the fleet away and return once the blast hits. if there are only 2 phase lanes, move 2 planets away, if there are more, pick on, the more planets the less chance he has of hitting your fleet

Which actually hurts you too, since the new Novalith brings down the max planet population with each shot for quite a long time. So if you colonize shortly after nuking it, you'll basically have planets with no population for a while.

Ok, I am guessing the one the OP is talking about it the Kostura.  So, if you see the war head coming toward you, jump your ships away from that gravity well.  It's that simple.  Also, the Kostura is completely offensive in nature, so if you go on the offense at one of their worlds (or a neutral world) they cannot fire at you.  ALso, sending a suicide fleet to destroy them is a good idea.  Or the labs.  But honestly, just take out the weapons as they are a significant amount of economy.

Also, shame on you for not scouting.  Building a super weapon means he sacrified in fleet.  Also, 8 weapons labs should give it away.  Now, if he had a better fleet and the super weapons, then shame on you because your ECONOMY SUCKS.