There is no option counter-representation so your code can't work. An invalid/unknown option to \cmpd is simply ignored.
I haven't added an equivalent of cmpd-label in v1.0 because I didn't deem it a very useful option but maybe I'm mistaken. (I hadn't thought that there was an actual use case for it...)
There is a workaround you can use: it's easy to add a command which overwrites the label that is assigned per default. For this the compound property counter-representation needs to be reset after the label has been declared (this needs expl3 syntax):
\NewDocumentCommand \setcmpdlabel {mm}
{ \chemnum_compound_set_property:nnn {#1} {counter-representation} {#2} }
A complete example could look like this
\documentclass{article}
\usepackage{chemnum}
\ExplSyntaxOn
\NewDocumentCommand \setcmpdlabel {mm}
{ \chemnum_compound_set_property:nnn {#1} {counter-representation} {#2} }
\ExplSyntaxOff
\begin{document}
\cmpd*{foo}\setcmpdlabel{foo}{bar}\cmpd{foo} and again \cmpd{foo}
\end{document}

\cmpd[cmpd-label=foo]{bar}very useful as some compounds just require to be referenced to with their common names: like d4T, AZT, ABC when you look at antiretroviral nucleoside analogous drugs or MOF-5, HKUST-1, UiO-66 when talking about metal organic frameworks - just to name two examples. – user49454 Apr 08 '14 at 07:50