This is mainly about Novaliths, because the Advent, and Vasari supewweapons wont wipe out the planet they hit. Advents Joy Gun just spreads culture, and Vasari superweapon disables structures, but does no damage to the planet itself.
There will be a cap on how many superweapons you can build. The amount will depend on feedback from beta testing.
Right now the counters to Mass Novalith Spam are.. Aux Govt for TEC (or equivalent for Advent/Vasari) Starbases! This is a MUST HAVE to protect you from loss of worlds during bombardment. Sure you will lose some pop, and income, but you will not lose the planet itself. You will not lose Capital Victory. Your planet will recover in time. However Aux Govt. wont protect you from culture flipping. Only broadcast centers, and the happy happy joy joy gun can.
Maxing out infrastructure to boost planet Hit Points wont hurt ether. Build Shields, and research techs that protect your population during bombardment. Like Crisis Recovery for TEC, Hardened Cities for Advent.
Go on the Offensive! Find the worlds with Novaliths. Listen to the anouncements. Watch where the projectiles come from. Find them, and Smite them! Even if you dont destroy the planet itself. Destroy the Novaliths! They blow up real good. This is where hit, and run fleets come in handy.