Short example illustrating the behavior:
user=> *clojure-version*
{:major 1, :minor 6, :incremental 0, :qualifier nil}
user=> (def f1 '(defn foo [^Integer x] ^{:bar 8} (inc x)))
#'user/f1
;; pr shows all metadata, as expected
user=> (binding [*print-meta* true] (pr f1))
^{:line 2, :column 10} (defn foo [^Integer x] ^{:bar 8, :line 2, :column 33} (inc x))nil
;; pprint shows some metadata, but not all
user=> (binding [*print-meta* true] (clojure.pprint/pprint f1))
(defn foo [^Integer x] (inc x))
nil
I have not dug into the details yet, but it appears that this may be because pprint uses pr to show symbols, but not to show collections. Thus pprint shows metadata on symbols, but not collections.
It would be nice if pprint could instead show all metadata, as pr does, when *print-meta* is bound to true.