The unexplained acceleration has been observed inside the orbits of Neptune and Pluto, thus it is unlikely that the terminal shock is having an effect. Dr. John Anderson, who is the principle investigator on this subject at the Jet Propulsion Labrotory, has discounted this explanation as well as the idea of uneven heat loss and gas venting, saying that all are too small to account for the observations. He does think that eventually a conventional explanation will be found.
I've read a fair amount on the subject and I am begining to suspect that indeed some new physics will be needed to explain the observations, though just what I don't know. It will be interesting in either case.