Good points. I don't think pairs are a code smell when used reasonably in situations where a pair of two values makes sense, like in your make-hash example. Ideally though I'd like to have a real, distinct (immutable) pair/association type separate from the cons/list and maybe use the dot syntax for that instead.

Deeply nested pair & list constructs that need to be unpacked with complex car/cdr combinations is what IMHO gets messy and I take the appearance of cddar & co in code as a sign that I should start thinking about using proper data structures.