Resolve Mypy errors in v3 branch

[jhamman]

The v3 branch needs some Mypy attention. As expected, our port of the zarrita code (see #1584) has left a number of mypy errors that would be great to resolve.

This ticket can be closed when:

• we have CI running against the v3 codebase
• we have zero mypy errors when checked in a github action

Marking this as help-wanted!

[jhamman]

This is feeling like a fairly high priority to start ticking off. For now, I've disabled the mypy checks in pre-commit (#1649) but this should be a short lived state.

[DahnJ]

I wanted to get into zarr a little and this issue had "help wanted" tag, so I picked it up here: #1692

I made a few choices in fixing some of the issues, hope it helps more than adds noise 🙂