Would it be possible to add this into the config:

Effects:
Smoke: true/false
Explode: true/false
Lightning: true/false
Flames: true/false
Bats: true/false

The above determine if the effects are defaulted to be enabled when joining the server or disabled.

I agree. This would make it a lot easier with the permissions, IMO.

Permission nodes are much more flexible, and since they default to all effects disabled it's not a concern to be using them. I'm not adding a redundant control over effects which would only cause further confusion when trying to enable them