Need type hints. This function does not really replace anything. Can we rename to something more self documenting? get_letter_by_letter or lookup_letter_by_letter. Alternatively could we have a single function instead of two functions? get_letter or lookup_letter could start with isinstance(key, int) and return the right result if key was a str or int.

Please make this a list comprehension as discussed in CONTRIBUTING.md.

Type hints? Combine with previous function? Or replace with __index__().

It is too confusing to use the same variable as both a str and as a list. Can we replace lines 113 and 114 with:
chars = [char for char in text.upper() if char in self.key_string]
and then change the variable name in the lines below? We do not need to declare the type because CPython is smart enough to know that a list comprehension returns a list.

Comprehension please.

Doctests do not work in if __name__ == "__main__": so please bring back main().

The type hint is not really required here because CPython is smart enough to know that [] is a list. A useful type hint would be hill_matrix: List[int] = [] assuming that from typing import List was added above.

Please add type hints to function parameters and return values. This is where type hints are most valuable/helpful because in other locations CPython is often smart enough to determine the type from the context.