Enable more mypy error codes

Mypy has extra error codes you can enable.

Example config is `enable_error_code = possibly-undefined, deprecated` in the `mypy.ini`.

Would have helped with

- https://github.com/element-hq/synapse/issues/19779

and related

- https://github.com/element-hq/synapse/pull/19712#discussion_r3117020750 (if downstream users enabled `deprecated`, we could make use of `@deprecated` annotations)

This would also involve exempting or fixing up many places.