Please explain your feature request to the best of your abilities:

Looking for a way to disable nationzones in the nether while keeping it active in overworld and end.

I went looking into the code and it's not going to completely disable it (your players would still see chunk notification messages saying they've entered a nationzone,) but you can disable the nation zone protections by using a permission plugin to give players in the nether the towny.admin.nation_zone permission node.

That should set work until I (or someone else) can add a proper world toggle for nationzones.