One example I remember is Pidgin storing its passwords in plain text in $HOME. They could have encrypted them with some hardcoded string, and made a lot of people happy that they would no longer grep their $HOME and find their passwords right there. However this had the side effect that now people were dropping the ball and sharing their config files with others. Or forgetting to setup proper permissions for their $HOME, etc.
In addition, these layers of obscurity are also not overhead free: they may complicate debugging, hey may introduce dangerous dependencies, they may tie you to a vendor, they may reduce computing freedom (e.g. Secure Boot), etc.