Would zsh still protect me if the script explicitly uses Bash (i.e. #!/bin/bash)? Sorry if this is a dumb question, I'm unsure how shells work when calling other kinds of shell scripts.
No. If the script has the #! set as /bin/bash, then it will run as bash.
zsh is an interactive shell. It is not to replace #bash as system shell as I know.
Zsh doesn't have to be used interactively.
It's also excellent for scripting, and has far more features than bash.