I attempted to disable the deer several times but they continue to spawn. Config is below.
mysticalworld.txt
Edit: The same issue applies to foxes as well

Hm, this might be an issue with the config just not being read then... I'll look into it.

I found the issue, custom mob spawner was overriding the config and making them spawn. It's working fine now:)

Oh, I'm glad! There have been instances where config values aren't being read which were hard to sort out. Glad it was so simple.