Hi James and Welcome. My Name is ***** ***** I look forward to assisting you today with your question.
I'm sorry about your loss. I know it is very frustrating but you are not alone. Many people are experiencing this same kind of issue with Notes. This mainly happens when you sync the Notes with multiple devices. Glitch in one device could result in loss of notes from other devices. There is no way to prevent them but precaution you can make is backup to email or other notes which you are already doing. And Yes, there is no specific reason for this. It just happens without any reasons. Probably a syncing issue.
I myself have Mac, iPhone and iPad and I don't use Apple's Notes. I'd strongly recommend to switch to EverNote or OneNote.
I myself use OneNote which is completely FREE and doesn't require any subscription. It is far more reliable than Apple Notes and not only that but also it is supported on multiple platforms like Android, iOS, PC and Mac where Apple Note's isn't. You can only use Apple notes on Apple devices (or through browsers). There is no native app for Android or Windows PC.
If you want, I can help you to setup OneNote or Evernote on your Mac.
If you have any questions or would like any additional information, please don't hesitate to ask
iCloud does save archives of old Contacts, Calendars and Bookmarks except Notes. There is no backup of Notes anywhere in iCloud except in Notes app. If they disappeared from there, then you can't recover them. Sorry.
Go to www.icloud.com
Login to your iCloud account and click Notes. Do you see the disappeared Notes there ? If not, then I'm sorry they are gone and there is no way to get them back.
I'd still recommend to switch to Ever Note or OneNote. Because these are multi-platform applications which is the biggest feature that kills Notes. You will be able to access your notes from any devices or from any browser.
I've myself experienced many issues with Notes and the organization is very bad is Notes. This is the main reason I switched to OneNote. I've never lost anything from OneNote not only that I can save different notes in different notebooks and also I can make multiple copies of the Notes within the app (in 2-3 seconds). This is great feature if you would like to make periodic backups of different versions of notes you are writing. Believe, once you switched to OneNote or Ever Note, you will not go back to Apple Notes.