Great questions:
- Encryption using PGP
- Use auto-fill mode 3.Use the TreeMacs package
- Org mode does bold, italics etc.. Colours in Emacs have semantic meaning and are automated through a theme.
- Use a note-taking application, such as Denote or Org Roam
- Org mode can be exported to many formats. Your documents are in plain text, so conversion is trivial. Aesthetic colouring is managed through export templates if you build a website, book etc.
- Use Org mode
My website Emacs Writing Studio explains most of what you like to achieve.