Bukkit

Currently any player can make and use wither arrows, even if they are disabled in the configuration file, and even if that user does not have the permission node to use them.

Checked it real quick, Found a missing { } for the wither arrow that would explain permissions doing nothing, so that should be fixed. However I don't see anything that would stop them from not being able to be disabled.

Please make sure you didn't accidentally added a space, tab or misspelled "false" or check if it really says "Enabled: false" .

I'm pretty sure that the only reason for you not being to disable Witherarrows from being crafted is because of a config error, either spelling or a tab/space. All arrows are handled the same way, you could basically just add another section with any name you want and it would be crafted as long as the "Enabled: true" is there, a name and lore. It would not do anything but that's just as an example of how I coded this. Nothing is hard-coded, it's pulled from the config.