The Justices are careful not to applaud any of the issues that could involve them.
They applauded for Sandra Day O'Connor, the military, etc....anything that honors an individual.
But they do not applaud "issues". Please don't read anything into this.
Justices historically do not applaud during the SOTU in order to appear impartial. Excepts occur of course, like the applause for Justice Alito.