It seems that any defined custom columns is available whether the script defining it is enabled or not.
By available, I mean available with values, not only that the column is shown in the columns list.
Currently the enable/disable checkbox only determines whether the script responds to events (OnBeforeFolderChange, etc). Since OnInit has to be called whether the script is enabled or not, any columns or commands the OnInit method adds are always active.
We may change this in the future although it's complicated and therefore not a high priority.