In my years as a dev I haven't found many true dependencies on Bash/Zsh. For Ruby, rbenv and other solutions worked. For Python, there was virtualfish to make virtualenvs work properly. Although now pyenv works out of the box with Fish. Other than that, simply adding a shebang to scripts is sufficient.

That being said, I don't go and convert the shell of all my AWS instances to Fish. I just keep my local shell as Fish.