In my spare time (i.e. not paid Element time) I've been working to add type annotations to pynacl, see pyca/pynacl#660. This is almost done, and the maintainer is keen to include them in a new minor release, "in the next few days/weeks".

Once there's a release, we should remove pynacl from the list of imports we ignore in Sydent's mypy config. Then we should fixup any complaints. The same also holds true for signedjson and sydent (see matrix-org/sydent#478).