It looks like in earlier versions (from comments on reddit) of the mod could or should have had the ability to disable the spider nest dungeon. I'm running version 2.1.0 for Forge for Minecraft 1.18.2, and the only option I see is min and max start height.

Trying to change these values to -128 to try to effectively disable it, seems to break world gen.

Can be done by creating a custom datapack to override spawnable biomes for the dungeon type.