> There are over 3,000 emojis defined in unicode, which is a very large vocabulary in which to become expert.
Most of those emoji aren't commonly used. There's a falafel emoji; no one's going around adding a falafel to the end of their messages trying to impart some hidden meaning.
> There is no well-defined meaning for any of the emojis, even the "simple" common ones.
There's also no well-defined meaning to a shrug or an eye-roll, but it's still a useful way of communicating emotion. Semantically, an emoji isn't used like a word. It's used like a gesture or facial expression. In practice, the message is usually quite clear — clearer, in fact, than if an emoji hadn't been used, since in the absence of tone-of-voice and body language text can itself create ambiguity.
> They mean different things to different subgroups, and act as an "in-group" credential in many cases.
Do you have an example of an emoji meaning different things to different groups? In my experience they have a pretty consistent meaning across our culture — even the more abstract ones, like an upside-down smile. The only barrier is "whether or not you're familiar with the typical meaning," and that's the case for any expression or colloquialism. If I say "they're like two peas in a pod" and you have no idea what that means, that doesn't mean it's an in-group signifier. Granted, familiarity with emojis correlates with age, but that's the same with any linguistic shift.
> They are visually very indistinct, and can be difficult to distinguish one from another for people who have less than perfect vision, or color-blindness.
I'm sure there are accessibility options which people can configure on their phones to minimize this. Large-text mode, for instance, or a high-contrast emoji font. Text itself is a medium which isn't very accessible to vision-impaired people, and we have developed solutions for that.
> For people with autism or other non-neurotypical processing they can be completely unintelligible, rendering the communication even less successful than "traditional" language.
Autistic people also have trouble understanding the meaning of facial expressions and of metaphors sometimes, but that doesn't mean that those shouldn't be used in conversation. It just means that everyone should know their audience.
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I don't think you've raised any serious practical issues — they seem to be all special cases, such as "what if you're talking to an autistic person or a blind person or an older person." Under those circumstances I would communicate differently, same as if I were speaking to a deaf person, or emailing a blind person, or talking to someone with poor English skills. There is no universally-viable way of communicating, but emoji typically reduce ambiguity and add layers of expression to a message, so in most cases they're a good choice.