You could just go to the GalaxyScenariodef file, hit CTRL+F, type in the text "_TECHORBITALCANNON" and just delete those. You would have to revise the planetItemType count, but that is just counting.
The GalaxyScenarioDef controls nothing about what players can build. All it does is control what sorts of objects get spawned at the start of the map.
The real way to do it is to do the following.
1. Get the reference data.
2. Make a new folder in your mod folder called "No Super Weapons". In that folder create another folder called "GameInfo". In the reference data you downloaded, find a file called "PLANETMODULE_TECHORBITALCANNON.entity". Copy it into the GameInfo folder you just made.
3. Open the "PLANETMODULE_TECHORBITALCANNON" file in notepad. You can change all the stats of the Novalith cannon here. I recommend finding the line "planetUpgradeSlotCount" and changing it to 99, as it doesn't seem to cause the AI any trouble.
4. Repeat with the PLANETMODULE_PSI and PLANETMODULE_PHASE Orbital Cannons.
5. Enable your mod and it should be impossible to actually play superweapons.
Technically the best way might be to just disable the research for the superweapons, but you may run into some AI issues as it probably expects to find a superweapon research available to it.