Now, the question is, how did this happen in the first place?
Good question and one to for which I don't even have a guess, much less an answer.
I should point out the ability to delete apps that come
"in the box" with MacOS has gone back and forth over the years. Many Apple apps, such as Mail, which were deletable (and re-installable from the App Store) in High Sierra and Mojave are no longer deletable in Catalina. This has nothing to do with their location in the system area, instead because they, or at least some of their functional routines, are used in other Apple or third-party apps. So deleting an app as innocuous as Notes could potentially prevent another app from working correctly, if at all. You could spend a lot of hours reading crash logs to determine the cause of such failures.
If you don't want to
see your unused apps, you could move them to another folder that is out of the mainstream or possibly even invisible, but deletion is not a good idea.
