This weekend I upgraded a Jira instance from one LTS release to the next (8.13.1 to 8.20.1). 

Everything appeared to go well, but shortly afterwards users started complaining: Jira is not emailing certain users.

I checked, and sure enough: there's a situation where Jira 8.13.x and all prior releases would email, but Jira 8.20.x will not.

Specifically, this affects users like this one, who are not in a group like jira-users blessed with 'Application access':

The 'helpdesk' user here is, per Crowdsourcing triage: A useful pattern for Jira issue ownership, an account that never logs in but does get emailed.

What should happen if a new issue is created, assigned to 'helpdesk', or with 'helpdesk' as a watcher?

The 8.20.x behaviour is actually correct. An account without Browse permission shouldn't get emails. Yet this important bug fix is not one of the

fixed between 8.13.1 and 8.20.1 - at least, that I can see.

Anyhow, to know whether your Jira has any user accounts like this, run the following SQL (Postgres-flavoured):

select user_name FROM cwd_user JOIN cwd_membership ON child_id=cwd_user.id JOIN cwd_group ON cwd_group.id=cwd_membership.parent_id WHERE cwd_user.active=1 AND cwd_user.id not in (select child_id from cwd_membership JOIN licenserolesgroup ON licenserolesgroup.group_id=cwd_membership.lower_parent_name);

If you get output, that's bad - those users will stop getting emails in 8.20.x+. Time to fix your group memberships, or bless the group your users are in (here 'MyCompany') with application access.