It depends on what you're scripting, some things really are expressed best in the shell.
But tools like perl, python and ruby aren't nearly as universal as you'd like them to be. Obviously if you maintain the box and are deploying an app, they're trivially available. But if you're shipping software to be installed on end user boxes of unknown configuration, they're a dependency that can bite you. That's why things like self-extracting archives and shell-based initscripts persist, even though they look ugly to modern eyes. They do what they need to do very well, and they do it universally.