Every faction has the ability to research and build a starbase upgrade that prevents losing the planet from bombardment while the Starbase is alive, and this includes from Novalith cannon strikes. Thus the best defense is to build these on your most valuable worlds, though you will still lose some population with each it.

Also if this is Rebellion, technically the AI cannot build superweapons on every planet. There is a limit of 1 superweapon per 4 planets, or possible 1 per 2 planet if it is a TEC Loyalist player with Novalith deregulation researched.

If everyone is running the same mod, you can play multiplayer together.

This is why i like to play advent against a nova-spamming TEC player. They have an ability called synergy where if you build enough turrets (i think its 18), they encase the planet in a giant collective mind force field that makes it immune from planetary bombardment. All the pro players online do this, and it works extremely well.

I would also like to add that the planetary defense shield can be very useful in defeding against novas.