"so it's true that an email may not get sent for every individual endorsement, mention, or reply you receive."
This is a woeful understatement and I expect you must understand that it is so. I mean, thanks for speaking up, but why'd you bother? To suggest that this was a matter of people missing an email here and there? It isn't.
This is an issue of only occasionally getting the one out of many that your system would otherwise generate. I seem to get lots of sales email from Drop trying to sell me something, so I know you guys aren't really limiting all email -- you're just limiting community related email, and not even saying so until someone speaks up, which is distinctly sketchy behavior. Some people call that soft power, but no one calls it brave.
just reframing it: you have a menu that allows members to control what sort of messages they can get, and hence already have the means at hand to let people choose what’s spam to them and what they want to see. If it’s about bandwidth there are better options than simply not sending stuff w/o letting folks know otherwise.
I would counsel you to try and game your community a little less and embrace their behavior a little more. Don't suppress content and don't let 'bugs' linger that sure seem like they're underhanded features. If it gets so far that someone has to go to an outside source to document that it's still happening, nobody wins that one.