After suggestion from @user3439894, I had tweeted Apple Support and here is their answer:
We love feedback. If you don’t see the Apple app you wish to leave feedback for, you can leave feedback by choosing the device you are using here: http://apple.co/Feedback
So, following that, I had posted the feedback using one of my devices as a channel, explaining ...
As long as there are notes in Recently Deleted, the folder will be there.
There's nothing much you can do about system folders. I tend to ignore them unless required. Or not make a folder at all. This keeps everything simplified(relatively).