Why do I get email notifications about comments that WordPress has already determined are spam?

Disclaimer: I wrote parts of the Akismet WordPress plugin, though not the parts in question here.

Is Akismet failing to connect to the Akismet service, notifying me, and retrying later?

Yes, this is exactly what happens. If Akismet doesn’t get a valid response from the servers, it reschedules the check for 20 minutes in the future. In the meantime the post is considered held for moderation, since its actual status (ham or spam) is yet undetermined.

If so, is it possible to turn off the initial notification email in this case?

I regret that I don’t know of any good way to do this for only this circumstance. But I have never had so much spam making it as far as Akismet that this happens more than once or twice a week, so I’ve never been bothered to make the attempt.