How do I ensure new dependencies added to the info.yml of an existing enabled module are picked up?
I think you are mixing dependencies to modules with dependency to libraries. Your code adds a PHP module dependency to core/jquery, and I don't know any module of this name.
(When in module.info.yml)
If you want to add a (JS or CSS) library dependency, use the libraries: key and not dependencies:
(When in module.libraries.yml)
Remember that just defining a library does not automatically load it, you still must add it in module.info (or load it dynamically)