The Hypocrites’ hugely popular Chicago-bred production of Gilbert & Sullivan’s “Pirates of Penzance,” featuring a new adaptation by director Sean Graney and musical arranger Kevin O’Donnell, will be setting sail for its second visit to the American Repertory Theater (A.R.T.) in Cambridge, Ma., where it will be the final production of that high-profile company’s 2012-2013 season at the Loeb Drama Center. The 80-minute show, “full of bathing beauties, philosophizing pirates, and remarkably short shorts” was the runaway hit of the Cambridge company’s 2012 Emerging America Festival.