Q: Where are the notes in Apple Mail?

I wasn't aware there were Notes in Mail.  I searched through the Help section and found nothing.  It doesn't appear they exist anymore.

The following from iCloud: Notes overview may help:

Notes on your devices

When you make changes using Notes on iCloud.com, they appear automatically in the Notes app on your iOS devices and Mac computers where you set up iCloud for Notes, and vice versa. You can also view your up-to-date iCloud notes in Microsoft Outlook on your Windows computer set up for iCloud Notes.

However, if you upgrade your iCloud Notes account on an iOS 9 device or a Mac with OS X v10.11:

• Your notes on those devices and on iCloud.com aren’t kept up to date with notes on any of your devices with iOS 8.4.1 or earlier, OS X v10.10.5 or earlier, or Windows.
• Your notes are no longer stored in your @icloud email account.

Where did they go?

To a separate application called "Notes."