How to remove Notepad from the applications list?

I had that problem too some months ago, and I remember I had to delete some .desktop files that were inside the $HOME/.local/share/applications folder. I think you should delete any file that has notepad as part of its name, and also you should try to delete (or move somewhere else) the files wine-extension-*.

Modify /usr/share/applications/wine-notepad.desktop, adding the line:

Hidden=true

There is a bit more information about what that does here. Alternatively, you could probably just delete that file instead.