When comparing Org mode for Emacs vs Zettlr, the Slant community recommends Org mode for Emacs for most people. In the question“What are the best knowledge base systems for personal use?” Org mode for Emacs is ranked 3rd while Zettlr is ranked 12th. The most important reason people chose Org mode for Emacs is:
Org mode started out as a simple outlining/note taking app. Then each outline heading can optionally be a TODO list item. And if you desire, you can add SCHEDULE and DEADLINE dates. (Schedule being the date you'd like to start the item.) You can customize the TODO states to add things like DELEGATED, WAITING, BLOCKED, etc.
Specs
Ranked in these QuestionsQuestion Ranking
Pros
Pro Can be as simple or as complex as you want
Org mode started out as a simple outlining/note taking app. Then each outline heading can optionally be a TODO list item. And if you desire, you can add SCHEDULE and DEADLINE dates. (Schedule being the date you'd like to start the item.) You can customize the TODO states to add things like DELEGATED, WAITING, BLOCKED, etc.
Pro Libre/open source
Pro Cross platform
Emacs runs on all platforms, Windows, Linux, OSX, even Android and IOS

Pro Exports data to PDF, LaTeX, HMTL and other
You can even build presentation or blog from your data

Pro Supports tables with formules (quite powerful!)
Pro Plain text data storage
Future-proof.
Pro Inline image displaying
Pro Free but copyrighted
Pro Fast interaction
Once muscle-memory sets in, can be much faster to use than a point & click program.
Pro Uses Emacs
Pro All apps
Pro Focuses on writers
While many Markdown editors don't offer specific support for a certain type of workflow, or offer features for scientific workflows only, Zettlr offers features that help the writing process of journalists or researchers in the arts and humanities. It's a lot more text-focused than most editors.
Pro Citation support
While it supports a diverse range of syntax (chart, easy image insert, etc.) found in other editors, the great citation support made it possible to write real articles. Citation from Zotero and Mendeley can be inserted easily which is a huge plus.
Pro Almost perfect
This is the best option, still not perfect, there are some bugs like creating / editing tables and resizing images, but the PROS destroy the CONS, easy quotes, WYSIWYM , attachments tab (supports attaching and opening links to any file), table of contents, TAGs, easy hyperlink between files (same as citations), export to many formats (like Word, HTML5, PDF)...
Pro Renders math in-place through KaTex
Cons
Con Obtuse documentation
The documentation assumes a level of understanding of basic Emacs usage that not all users may have.
Con Complicated to get started
Con Difficult to use as a database
For example, if you need to quickly populate client details on quotes, unfortunately its easier to find, copy & paste.
Con Not suitable for normal users
Not even a majority of software developers can be bothered to use Emacs (or VI, for that matter).
Con PDF export can be difficult
Latex assumes you're a (compliant) student, have to do a lot of research to get what you want out of it.
Con Uses Emacs (for those who prefer vi, menus, etc.)
Con Obtrusive, like someone WITH CAPS LOCK ON
Too loud, too much going on, and definitely an in-your-face sort of feeling.
Con Large, slow, can't open just a single .md file
