And once you've used that API to download and tag everything, what tools do you use to interactively view the results, run search queries, apply patches to local trees etc?

If your on-disk format is an Mbox or a Maildir, you can use tools like notmuch and its emacs integration to do it.

Now don't get me wrong; I love GitHub. I host all my projects there, and I prefer PRs+issues to mailinglists in almost all cases. But for massive projects like Linux, a mailinglist (and associated tooling) scales better, in my opinion.

Which eventually will change, and you have to update everything. Or the company disappears and you have to move somewhere else.

Email is just email. You write SMTP/IMAP clients today and they'll continue to work for a long time, probably longer than most platforms with APIs online today.