I sent an email to shntool's author a while ago asking him for a new version to deal with the changes to wavpack. I haven't heard back or seen any movement, however.

I had a look at the source code for the shntool wavpack module. From what I can tell, the only think in there preventing shntool from using the new wavpack is that there is a line of code that tells shntool to exit if wavpack has a version number greater than 3.

Unfortunately I am not good enough with C++ to be sure that this is the only thing stopping shntool, or to change this and make a new compile. Perhaps some intrepid soul here could have a look at the source code and help us out.