One could extend the js/Date prototype with a setNanos/getNanos method and call them accordingly. I'd offer to implement that but the cljs.reader/parse-and-validate-timestamp function scares me, any objections to rewriting that?
As for the js/Date extension, thats easy enough:
(set! (.. js/Date -prototype -setNanos) (fn [ns] (this-as self (set! (.-nanos self) ns))))
(set! (.. js/Date -prototype -getNanos) (fn  (this-as self (or (.-nanos self) 0))))
Not sure if its a good idea though, messing with otherwise native code might not be "stable".