Dipping a powerhead should be fine. Most of the dips I have used recommend flow while dipping (i.e. a powerhead in the dipping container).
That said, when I get used equipment I thoroughly clean it (which usually negates the need to dip). I would take the powerhead apart and scrub it down. If there is anything caked on, I would soak those parts in vinegar overnight. I only recommend soaking hard plastics in vinegar though.