It's not "wrong" to present it to readers verbatim (i.e. not rendered to HTML), since Markdown is a codification of existing plaintext conventions, and was designed to look good verbatim. In other words, though it is often used for, it is not solely a vehicle for generating HTML.
And people started to have auto pasted ascii art.
That’s the point where emoji is a more concise, explicit and less cumbersome system.
We should see emoji as standardization and putting a business tie on chaotic expressions to pass them down the line in a limited amount of bytes.
I can use ":-)" to punctuate a joke, lower the tension in a critical message, or react to a cute picture. In each of these contexts, the smiley gets translated to different reactions which are still the property of me and the person I'm communicating with, particularly if we know each other in person. By using the plain ":-)" I am expressing my own sense of humour, my own way of being tactful, or my own way of smiling at a cute cat precisely because the smiley is so abstract. Alternatively, when I see one of my friends using ":-)", I will picture their own expressions, their own faces.
However, now with emojis, we are subject to the preferences of arbitrary designers and UX teams working for Apple, Facebook, Google, etc. and the latest trends in the small circle of trendsetters who have any influence. Each reaction has its own emoji or limited range of emojis, and the way of expressing playfulness, empathy, or reaction to cuteness has become commodified and standardised in sets of childish faces which have also become saturated by their overuse in marketing. I am expected to no longer express shock with ":-o", but with an overreacting Munch-scream-lookalike. Laughing now comes in pre-ordained grades, with anything less than "sideways with tears" seen as understated.
In summary, I feel that by being expected to chose between a pre-ordained set of designed smileys we are oursourcing our emotional range.