FP languages also rely heavily on partial pattern matching, type classes with vtable-style indirection and even GC for cycle collection. Closures in FP languages are boxed, too, almost without exception.
In Haskell, even integers are boxed by default. You don't observe many of the problems of references due to their immutability, but this isn't to say they're not there. The "value-heavy" language closest to FP I know of is Rust, and many functional idioms are plain irritating to use because of it.
Maybe Clojure is different, but I'd be surprised. Perhaps you were in disagreement about the use of the word "value" in "value type", which I meant in the D or Rust sense of a stack-allocated, indirection-free type.