Set which DCC tools are available for a project

The default configs include DCC apps we don’t use (nuke, mari)

Where do I remove the unwanted dcc apps from the config?

If you want to limit DCCs for a certain project, and are using Software entities in Shotgun, they have a field Projects, by which you can filter them for each project.
I guess all new setups use Software entities. If you want to completely remove those DCCs from everywhere, just delete the entities.
It depends on your config, though.