Ok, after trying many things, I guess found a solution.
First, the problem was very similar to the initial case, endless spinning synchronization icon and unreliable note numbers on various devices (Mac, iPad and iPhone).
The main reason was I guess, I had imported approximately 3.000 notes from Evernote as an ENEX file. The notes were successfully imported to Apple Notes on my MacBook Pro, successfully synchronised with iCloud and iPhone. But I had an endless sync icon on my iPad even after days..
What I did, I found the Exporter app from App Store which targets to export Apple notes of local folders as ".md" files with separate attachement folders. This app exported my whole library where ~10s of notes were "failed to export". After Exporter finished operation, it generates a log page where you can see the export failed note titles.
I found all these failed exports (many of them were notes with embedded TIFFs) and removed from Apple Notes, the iPad finished synchronization and all total number of notes on various devices were same.
Hope this small trick works for you.