Equation number referral doesn't appear within the empheq/array environment?

The main problem is that empheq redefines \maketag@@@ because it need to separate the display from the eqn numbers. But \eqref also make use of this macro to typeset the reference to an eqn numbers. The fix below seem to do the trick and will be build into the next empheq release

\makeatletter
\MHInternalSyntaxOn
\renewenvironment{empheq}[2][]{%
  \let\savedmaketag\maketag@@@
  \renewcommand\eqref[1]{\textup{%
      \let\maketag@@@\savedmaketag%
      \tagform@{\ref{##1}}}%
  }
  \setkeys{EmphEqEnv}{#2}\setkeys{\EQ_options_name:}{#1}%
  \EmphEqMainEnv}{\endEmphEqMainEnv}
\MHInternalSyntaxOff
\makeatother

The problem goes away if you use (\ref{whatever}) in place of \eqref{whatever}. I have no idea why this happens, though.