I'm not really defending the notion, only guessing why Apple chose to do it this way, and speculating in general, because I'm in the mood for it. But, it is, after all, Apple's MO, to hide the nuts and bolts when possible. Especially if they are easily broken.
The Notes folder in email is a poor workaround at any rate. It's basically flawed. Unfortunately it's also not easily fixed. At least not for non-iCloud services.
It's what Apple originally chose with it's own OS X Mail app; where the folder was accessible but also safely editable (because they could could control what happened. It also made sense, because the Notes function was a part of Mail, not a separate app. This legacy is why Apple (probably) chose to sync Notes on the iPad this way.
When Apple introduced Notes in OS X (the desktop) and in iCloud, they did away with the Notes folder syncing. It's a huge improvement.
However; there is no standard that lets them do the same thing with Yahoo! and GMail. While these services have their own Notes functions, they don't offer a way to sync. Or at least they don't offer an internet standards way of syncing notes (if there is such a thing). Though, in the case of Google, I suppose they might be able to do something with Google Drive.
So, we are left with what is basically a legacy workaround for those services. Whether it should be hidden or not is a personal thing. Some people hate the idea of not being able to do anything they want. Other's would prefer at least the illusion of simplicity. You can't please everyone.
Your argument for keeping it visible has merit. However, in most cases when Notes disappear from the Notes app, they disappear from the synced folders as well. It's rare that they can be recovered from there. And as for editing the notes in the Notes folders, I recommend you don't. The files stored in that folder are not standard emails. It's very easy to wreck the formatting if you edit them in the email app, and make them useless in the Notes app.
For myself, I don't depend on the Notes app. Of all the app Apple has provided on iOS, it has got the worst history for losing data. Much of that is probably because of the way it syncs data with folders in other services/apps that it can not prevent from being corrupted by those services and apps. Not that iCloud Notes have been doing much better. Cloud services is still something Apple has problems with.
The Notes-IFTTT-Evernote trick I mentioned isn't really about backing up my Notes for me (though you can do that). It's a way of being able to dictate short notes (in a log form) into Evernote using Siri.
Anyway, I babble on and on.