This program will actually, properly, in a WYSIWYG manner, from a Mac, export every note in your Apple Notes app to PDF, while preserving (inasmuch there are special characters that might need adjusting) the folder hierarchy and notes titles, and avoiding duplicate filenames.

Unfortunately, it works by sending keyboard events to notes, because I have not succesfully managed to get the AOSC API to properly export attachments in all cases; in my own case, about 1 in 4 pictures or other attachments just won't export (usually, it seems to be somehow related to iCloud), at all. Indeed, in this incarnation, some things are still probably lost (e.g. if you attached a PDF inside a note; also, images in 'small' format will end up in the PDF, as, well, small in size.) But at a minimum, all notes including text, formatting Apple Pencil markup and images, will end up in PDF as you would see them in notes. Which makes it a useful backup when you primarly use notes as a journal or dumping ground.

One day Apple will give Notes a proper API like the Calendar and other things seem to have now.

• Open the Apple ScriptEditor on your Mac
• Create a new script, change the type to Javascript
• Copy and paste the content of ScriptEditor/ExportAllTheNotesToPdf.applescript into it (you really should not trust scpt files...)
• Ensure that Notes app has no open Windows or save dialogs, etc.
• Run the Script, choose a destination folder, wait.

For best results, choose a new empty folder!

• first, unlock your notes
• then in the script ExportAllTheNotesToPdf, near the top of the file set the constant skipPasswordProtected to false

Due to the way this sends keys and interacts with the clipboard, once the process starts, avoid using the computer to do anything else!

It can be aborted by hitting the Stop button in the Scripting App.

You should probably make sure you have a backup of your iPad or iPhone first; this script is working for me, but there is a chance if something goes wrong it could paste text over all your existing notes!

• enumerate the attachments in the metadata file
• add a UI to allow a single folder to be selected, or other kinds of filtering
• maybe crack the problems with generating HTML and exposing the attachments

The only script you need is ScriptEditor/ExportAllTheNotesToPdf.scpt, all the others are experiments where I was trying to find a way to use the Notes applescript API to get the underlying content and enumerate all the original attachments, and save the result in HTML as I was originally hoping to convert it to Markdown and at the same time preserve attachments in separate files. However, a good chunk of my notes just failed.