That line you linked is specifically for reading an individual character value (like \a) - as a single character it's not possible to represent both parts of a surrogate pair, so this seems correct (a Java char is an int).
However, you can use surrogate pairs in strings, which is how you would most commonly use them, and that works fine.
$ clj
Clojure 1.12.3
user=> "\ud83d\ude0d"
""
I believe surrogate pairs are not currently allowed in symbols or keywords, that's maybe something that could be extended in the future, but I haven't seen anyone looking for that yet.