I am assuming clj-kondo does a one pass analysis of the code. So if a function is called before it's defined, then it is marked as not found. I think I saw this for the first time today, when using clj-kondo with Emacs. Just curious if this assumption is correct. I get so used to the REPL let me do any order in the source code file so as long as things are evaluated in the running REPL.

That's true, one pass, just like Clojure itself

Same here, I usually have rich comment blocks scattered around the source file as REPL experiments / documentation, and which reference functions defined much later in the file - there I insert (declare <function>) in the comment block to get around clj-kondo's warnings