documentclass{scrbook}

usepackage{chemmacros} % this loads xparse, which supplies NewDocumentCommand{func}{argspec}{code}

NewDocumentCommand{aeq}{m}{#1~eq.} % equivalents

begin{document}
aeq{2.5} % prints 2.5~eq.

aeq{0.03} % prints 0.03~eq., but I want to have it print 3~mol-%
end{document}

documentclass{scrbook}

usepackage{xparse}
usepackage{calculator}
usepackage{ifthen}

NewDocumentCommand{aeq}{m}{
    ifthenelse{lengthtest{#1pt > 0.1pt}}{#1~eq.}{
        MULTIPLY{#1}{100}{myaeq} % multiply #1 by 100 and store into myaeq
        ROUND[0]{myaeq}{myaeq} % round myaeq to 0 decimal places, because multiply does weird calculations
        myaeq~mol-% % print result
    }
} % equivalents

begin{document}
aeq{2.5} % prints 2.5~eq

aeq{0.03} % prints 3~mol-%

aeq{0.9} % prints 0.9~eq

aeq{0.1} % prints 10~mol-%
end{document}