Well, they already reduced the number of super weapons you could build to 4 in Rebellion to try and deal with the problem. A lot of players thought this was a bit extreme though, especially as the TEC Loyalists needed them so much, and that as a player its fun to use swarms of them. Thus in the next patch, the number of superweapons you can build will be based on the size of your Empire. Small Empires will only be able to field 1 or 2, large ones could build more than 4.
FYI to deal with Novalith attacks, build starbases on your important planets, and build the axillary government or equivalent upgrade, and you will not lose your planets to bombardment, including Novaliths. TEC shield generators can also reduce the damage and deaths the Novalith inflicts, by up to 70% full upgraded.
Also FYI the AI did use superweapons in the final patches of Diplomacy, without any limit to how many they could build. Also the harder AIs get a economic advantage, and Cruel+ AI get faster research, plus perhaps other noncombat benefits, allowing them to get superweapons faster and in larger quantities. Even if you can beat those AIs I'd say its smarter to stick with unfair AI, the harder ones are indeed not as fun to play against because its not even close to a fair fight. Try doing more challenging scenarios or give yourself restrictions (I.e. no building starbases, which the AIs suck against) to make the weaker AIs more fun. Or there's also online play if you want a real, smarter challenge.